Survivin, a protein that inhibits cellular apoptosis, and its modulation

ABSTRACT

The present invention provides the amino acid of a protein that inhibits cellular apoptosis, herein termed the Survivin protein and nucleic acid molecules that encode Survivin. Based on this disclosure, the present invention provides isolated Survivin protein, isolated Survivin encoding nucleic acid molecules, methods of isolating other members of the Survivin family of proteins, methods for identifying agents that block Survivin mediated inhibition of cellular apoptosis, methods of using agents that block Survivin mediated inhibition or Survivin expression to modulate biological and pathological processes, and methods of assaying Survivin activity.

STATEMENT OF RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No. 11/064,496filed on Feb. 24, 2005, which is a divisional of U.S. application Ser.No. 09/690,825, filed on Oct. 18, 2000, now U.S. Pat. No. 6,943,150,issued on Sep. 13, 2005, which is a divisional of U.S. application Ser.No. 08/975,080, filed on Nov. 20, 1997, now U.S. Pat. No. 6,245,523,issued on Jun. 12, 2001, which claims the benefit of U.S. ProvisionalApplication No. 60/031,435, filed Nov. 20, 1996, all of which are hereinincorporated by reference in their entirety.

FIELD OF THE INVENTION

The present invention relates to the field of modulating cell apoptosis,particularly agents useful to inhibit apoptosis, as well as todiagnostic and prognostic assays involving conditions in mediated by theexpression of inhibitors of apoptosis. The invention specificallyrelates to the identification of a novel human gene, tentatively namedSurvivin. Survivin encodes a protein, Survivin, that inhibits cellularapoptosis, particularly in cancer cells and embryonic cells.

BACKGROUND OF THE INVENTION

Regulation of cell proliferation by programmed cell death (apoptosis)maintains tissue homeostasis during development and differentiation(Raff, M. D., Nature (1992) 356:397-400; Vaux, D. L. et al., Cell (1994)76:777-779). This process involves an evolutionarily conservedmulti-step cascade (Oltvai, Z. et al., Cell (1994) 79:189-192), and iscontrolled by proteins that promote or counteract apoptotic cell death.Apoptosis also involves cell surface receptors (Smith, A. et al., Cell(1994) 76, 959-962), and associated signal transducers (Tartaglia, L. A.et al., Immunol Today (1992) 13:151-153), protease gene families(Martin, S. J. et al., Cell (1995) 82:349-352), intracellular secondmessengers (Kroemer, G. et al., FASEB J (1995) 9:1277-1287), tumorsuppressor genes (Haffner, R. et al., Curr Op Gen Dev (1995) 5:84-90),and negative regulatory proteins that counteract apoptotic cell death(Hockenbery, D. et al., Nature (1990) 348:334-336). Aberrantly increasedapoptosis or abnormally prolonged cell survival (Oltvai, Z. N. et al.,Cell (1994) 79:189-192) may both contribute to the pathogenesis of humandiseases, including autoimmune disorders, neurodegenerative processes,and cancer (Steller, H., Science (1995) 267:1445-1449; Thompson, C. B.,Science (1995) 267:1456-1462).

Specifically, for example, inhibitors of apoptosis, most notably of thebcl-2 family (Reed, J, J Cell Biol (1994) 124:1-6, and Yang, E, et al.,Blood (1996) 88:386-401), maintain lymphoid homeostasis andmorphogenesis in adult (Hockenbery, D et al., Proc Natl Acad Sci USA(1991) 88:6961-6965) and fetal (LeBrun, D. et al. (1993) 142:743-753)tissues. Deregulated expression of bcl-2 has also been implicated incancer, by aberrantly prolonging cell survival and facilitating theinsurgence of transforming mutations.

In addition to bcl-2, several members of a new gene family of inhibitorsof apoptosis related to the baculovirus IAP gene (Birnbaum, M. J. etal., J Virology (1994) 68:2521-2528; Clem, R. J. et al., Mol Cell Biol(1994) 14:5212-5222) have been identified in Drosophila and mammaliancells (Duckett, C. S. et al., EMBO J (1996) 15:2685-2694; Hay, B. A. etal., Cell (1995) 83:1253-1262; Liston, P. et al., Nature (1996)379:349-353; Rothe, M. et al., Cell (1995) 83:1243-1252; Roy, N. et al.,Cell (1995) 80:167-178). These molecules are highly conservedevolutionarily; they share a similar architecture organized in two orthree approximately 70 amino acid amino terminus Cys/His baculovirus LAPrepeats (BIR) and by a carboxy terminus zinc-binding domain, designatedRING finger (Duckett, C. S. et al., EMBO J (1996) 15:2685-2694; Hay, B.A. et al., Cell (1995) 83:1253-1262; Liston, P. et al., Nature (1996)379:349-353; Rothe, M. et al., Cell (1995) 83:1243-1252; Roy, N. et al.,Cell (1995) 80:167-178).

Recombinant expression of IAP proteins blocks apoptosis induced byvarious stimuli in vitro (Duckett, C. S. et al., EMBO J (1996)15:2685-2694; Liston, P. et al., Nature (1996) 379:349-353), andpromotes abnormally prolonged cell survival in thedevelopmentally-regulated model of the Drosophila eye, in vivo (Hay, B.A. et al., Cell (1995) 83:1253-1262). Finally, deletions in a IAPneuronal inhibitor of apoptosis, NAIP, were reported in 75% of patientswith spinal muscular atrophy, thus suggesting a potential role of thisgene family in human diseases (Roy, N. et al., Cell (1995) 80:167-178).

Therapeutic and diagnostic uses of nucleic acids that encode variousinhibitors of apoptosis relating to a member of the LAP family have beendescribed in the patent literature. See, for example, InternationalPatent Applications No. WO 97/06255, WO 97/26331, and WO 97/32601. Inparticular, the uses of such genes and gene products are contemplatedfor the novel protein and its encoding nucleic acid discussed below.

Recently, a novel gene encoding a structurally unique IAP apoptosisinhibitor, designated Survivin has been identified. Survivin is a −16.5kD cytoplasmic protein containing a single BIR, and a highly chargedcarboxyl-terminus coiled-coil region instead of a RING finger, whichinhibits apoptosis induced by growth factor (IL-3) withdrawal whentransferred in B cell precursors (Ambrosini, G. et al., Nature Med.(1997) 3:917-921). At variance with bcl-2 or other IAP proteins,Survivin is undetectable in adult tissues, but becomes prominentlyexpressed in all the most common human cancers of lung, colon, breast,pancreas, and prostate, and in −50% of high-grade non-Hodgkin'slymphomas, in vivo. Intriguingly, the coding strand of the Survivin genewas highly homologous to the sequence of Effector cell ProteaseReceptor-1 (EPR-1) (Altieri, D. C., FASEB J (1995) 9:860-865), butoriented in the opposite direction, thus suggesting the existence of twoseparate genes duplicated in a head-to-head configuration.

The present invention is based on the identification of a novel humangene which is nearly identical to EPR-1, but oriented in the oppositedirection. The antisense EPR-1 gene product, designated Survivin, is adistantly related member of the IAP family of inhibitors of apoptosis(Duckett, C. S. et al., EMBO J (1996) 15:2685-2694; Hay, B. A. et al.,Cell (1995) 83:1253-1262; Liston, P. et al., Nature (1996) 379:349-353;Rothe, M. et al., Cell (1995) 83:1243-1252; Roy, N. et al., Cell (1995)80:167-178), and is prominently expressed in actively proliferatingtransformed cells and in common human cancers, in vivo, but not inadjacent normal cells. Functionally, inhibition of Survivin expressionby up-regulating its natural antisense EPR-1 transcript resulted inmassive apoptosis and decreased cell growth.

SUMMARY OF THE INVENTION

The present invention is based, in part, on the isolation andidentification of a protein that is expressed in most cancer cells andinhibits cellular apoptosis, hereinafter Survivin or the Survivinprotein. Based on this observation, the present invention providespurified Survivin protein.

The present invention further provides nucleic acid molecules thatencode the Survivin protein. Such nucleic acid molecules can be in anisolated form, or can be operably linked to expression control elementsor vector sequences.

The present invention further provides methods of identifying othermembers of the Survivin family of proteins. Specifically, the nucleicacid sequence of Survivin can be used as a probe, or to generate PCRprimers, in methods to identify nucleic acid molecules that encode othermembers of the Survivin family of proteins.

The present invention further provides antibodies that bind to Survivin.Such antibodies can be either polyclonal or monoclonal. Anti-Survivinantibodies can be used in a variety of diagnostic formats and for avariety of therapeutic methods.

The present invention further provides methods for isolating Survivinbinding partners. Survivin binding partners are isolated using theSurvivin protein as a capture probe. Alternatively, Survivin can be usedas bait in the yeast two-hybrid system to screen an expression libraryand identify genes that encode proteins that bind to the Survivinprotein. Binding partners isolated by these methods are useful inpreparing antibodies and also serve as targets for drug development.

The present invention further provides methods to identify agents thatcan block or modulate the association of Survivin with a bindingpartner. Specifically, an agent can be tested for the ability to block,reduce or otherwise modulate the association of Survivin with a bindingpartner by contacting Survivin, or a fragment thereof, and a bindingpartner with a test agent and determining whether the test agent blocksor reduces the binding of the Survivin protein to the binding partner.

The present invention further provides methods for reducing or blockingthe association of Survivin with one or more of its binding partners.Specifically, the association of Survivin with a binding partner can beblocked or reduced by contacting Survivin, or the binding partner, withan agent that blocks the binding of Survivin to the binding partner. Themethod can utilize an agent that binds to Survivin or to the bindingpartner.

The present invention further provides methods of regulating theexpression of Survivin within a cell. Expression of Survivin within acell can be regulated so as to produce or inhibit the production ofSurvivin.

Blocking Survivin/binding partner associations or Survivin expressioncan be used to modulate biological and pathological processes thatrequire Survivin. For example, methods that reduce Survivin productioninduce apoptosis of tumor cells. Stimulation of Survivin production canbe used as a means of extending the culturability of cells or tissues.

The biological and pathological processes that require Survivin orSurvivin/binding partner interactions can further be modulated usinggene therapy methods. Additional genetic manipulation within an organismcan be used to alter the expression of a Survivin gene or the productionof a Survivin protein in an animal model. For example, a Survivin genecan be altered to correct a genetic deficiency; peptide modulators ofSurvivin activity can be produced within a target cell using genetictransformation methods to introduce a modulator encoding nucleic acidmolecules into a target cell; etc. The use of nucleic acids forantisense and triple helix therapies and interventions are expresslycontemplated.

The present invention further provides methods of reducing the severityof pathological processes that require Survivin. Since expression ofSurvivin or association of Survivin with a binding partner is requiredfor Survivin-mediated biological processes, agents that block Survivinexpression, Survivin activity or the association of Survivin with abinding partner, can be used in therapeutic methods.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-D show the identification of a complementary EPR-1 gene. A, B.Chromosomal location. A digoxigenin-labeled human P1 genomic cloneselected by hybridization with the EPR-1 cDNA, was incubated withmetaphase chromosomes isolated from phytohemagglutinin-stimulated PBMCin 50% formamide, 10% dextran sulfate and 2×SSC. The EPR-1-hybridizinggene was mapped in single-color labeling to the long arm of a group Echromosome (A), and in two-color staining with probe D17Z1, specific forthe centromere of chromosome 17 (B), to the long arm of chromosome 17(B), to band 17q25. C. Map of the antisense EPR-1 gene. A contigspanning 14796 bp was derived from two EPR-1-hybridizing P1 clones,subcloned in pBSKS⁻, and completely sequenced on both strands.Orientation of the map is 5′→3′ with respect to the position ofintron-exon boundaries (see below). Exons are solid boxes, a putativeCpG island upstream exon 1 is an open box. The translational initiationcodon (ATG) is indicated. Restriction sites are: B, BamHI, H, HindIII;P, PstI; S, SmaI; X, XbaI. D. Intron-exon boundaries of the antisenseEPR-1 gene. Positions of the intron-exon boundaries in bp are indicatedin parenthesis. The first nucleotide sequence corresponds to SEQ ID NO:5. The second nucleotide sequence corresponds to SEQ ID NO: 6. The thirdnucleotide sequence corresponds to SEQ ID NO: 7.

FIGS. 2A-C show the complexity and evolutionary conservation ofEPR-1-related sequences. A. Southern blot of human genomic DNA. Sampleswere digested with the indicated restriction enzymes, transferred toGeneScreen nylon membranes and hybridized with the EPR-1 cDNA, in 5×SSC,0.5% SDS, 5× Denhardt's and 0.1% sodium pyrophosphate at 65° C.Radioactive bands indicated by an arrow (7.6 kb BamHI, 7.5 kb XbaI andHindIII fragments of 15, 7.5, 6.4, and 3.7 kb) do not derive from theantisense EPR-1 gene in FIG. 1C. B. Southern blot of pulsed field gelelectrophoresis. High molecular weight human genomic DNA was digestedwith the indicated restriction enzymes, separated by pulsed field gelelectrophoresis for 20 h at 200 V with a pulse time of 75 sec,transferred to nylon membrane, and hybridized with the EPR-1 cDNA, asdescribed in A. C. Multiple species Southern blot. EcoRI-digestedgenomic DNA from the indicated species was hybridized with a 3′ 548 bpfragment of the EPR-1 cDNA, as described in A. For all panels, molecularweight markers in kb are shown on the left.

FIGS. 3A-F show the discordant tissue distribution of sense/antisenseEPR-1 transcripts. Northern hybridization was carried out on a multipletissue adult (A-C) or fetal (D-F) mRNA blot with single strand-specificprobes in 5×SSPE, 10× Denhardt's solution, 2% SDS, 100 mg/ml denaturedsalmon sperm DNA at 60° C. for 14 h. After washes in 2×SSC at 60° C. andin 0.2×SSC at 22° C., radioactive bands were visualized byautoradiography. A and B. EPR-1-specific single-strand probe. D and E.Antisense EPR-1-specific single-strand probe. C and F. Control actinprobe. Molecular weight markers in kb are shown on the left.

FIGS. 4A-C show the sequence analysis of Survivin and expression in celllines. A. Predicted translation of the antisense EPR-1 gene product(Survivin)(SEQ ID NO: 34). B. Sequence alignment of the BIR in Survivin(SEQ ID NOS: 8 and 21) and in other IAP proteins by the Clustal method.IAP proteins are identified by accession number, L49433 (SEQ ID NOS: 9and 22), TNFR2-TRAF signaling complex-associated LAP; L49441 (SEQ IDNOS: 10 and 23), apoptosis 2 inhibitor (Drosophila); P41436 (SEQ ID NOS:11 and 24), IAP gene from Cydia pomonella granulosis virus; P41437 (SEQID NOS 12 and 25), IAP gene from Orgya pseudotsugata nuclearpolyhedrosis virus; U19251 (SEQ ID NOS: 13 and 26), NAIP, neuronalinhibitor of apoptosis; U32373 (SEQ ID NOS 14 and 27), IAP-like proteinILP from Drosophila melanogaster; U32974 (SEQ ID NOS: 15 and 28), humanIAP-like protein ILP; U36842 (SEQ ID NOS: 16 and 29), mouse inhibitor ofapoptosis; U45878 (SEQ ID NOS: 17 and 30), human inhibitor of apoptosis1; U45879 (SEQ ID NOS: 18 and 31), human inhibitor of apoptosis 2;U45880 (SEQ ID NOS: 19 and 32), X-linked inhibitor of apoptosis; U45881(SEQ ID NOS: 20 and 33), Drosophila inhibitor of apoptosis. Conservedresidues are boxed, identities between Survivin and NAIP (U19251) SEQ IDNOS: 13 and 26 are boxed and shaded. C. Immunoblotting withanti-Survivin antibody JC700. Protein-normalized aliquots ofSDS-extracts of cell lines HEL (erythroleukemia), Daudi and JY (Blymphoma), THP-1 (monocytic), Jurkat and MOLT13 (T leukemia), or nontransformed human lung Lu18 fibroblasts, HUVEC or PBMC were separated byelectrophoresis on a 5-20% SDS gradient gel, transferred to Immobilonand immunoblotted with control non-immune rabbit IgG (RbIgG), oranti-Survivin antibody JC700 (Survivin). Protein bands were visualizedby alkaline phosphatase-conjugated goat anti-rabbit IgG and tetrazoliumsalts. Molecular weight markers in kDa are shown on the left.

FIGS. 5A-C show the regulation of Survivin expression by cellgrowth/differentiation. HL-60 cells were terminally differentiated to amature monocytic phenotype by a 72 h culture with 0.1 mM vitamin D₃ plus17.8 mg/ml indomethacin. Survivin expression before or after vitamin D₃differentiation was detected by immunoblotting with JC700 antibody, orby Northern hybridization with a Survivin-specific single strand probe.RbIgG, control non-immune rabbit IgG. Protein molecular weight markersin kDa and position of ribosomal bands are shown on the left of eachblot.

FIGS. 6A-H show the over-expression of Survivin in human cancer, invivo. A. Immunohistochemical staining of human lung adenocarcinoma withaffinity-purified anti-Survivin antibody JC700 (20 μg/ml). B. Inhibitionof JC700 staining of lung adenocarcinoma by pre-absorption with theimmunizing Survivin 3-19 peptide. C. Immunohistochemical expression ofSurvivin in squamous lung cell carcinoma, but not in the adjacent normalgland epithelium of the lung (C, arrow). D. In-situ hybridization ofSurvivin mRNA in squamous lung cell carcinoma with a Survivin-specificriboprobe. E. Expression of Survivin in pancreatic adenocarcinoma byimmunohistochemistry with JC700. F. Normal pancreas, negative forSurvivin expression by immunohistochemistry. G. In situ hybridization ofSurvivin mRNA expression in colon adenocarcinoma, but H, not in theadjacent non neoplastic colon gland epithelium (H, arrow).Magnifications are ×200, except G, ×400.

FIGS. 7A-C show the effect of Survivin on apoptosis/proliferation. A.EPR-1-regulation of Survivin expression. HeLa cells were transfectedwith control vector pML1 or the EPR-1 cDNA (which is antisense toSurvivin) by electroporation, and selected in hygromicin (0.4 mg/ml).Aliquots of vector control HeLa cells (Vector) or Survivin antisensetransfectants (Antisense) were induced with 200 mM ZnSO₄detergent-solubilized, and immunoblotted with the anti-Survivin JC700antibody. Molecular weight markers are shown on the left. B. Effect ofSurvivin on apoptosis. Survivin antisense transfectants (1, 2), orvector control HeLa cells (3, 4) were induced with Zn²⁺ ions in 0% FBSfor 24 h and stained by the AptoTag method with TdT-catalyzed dUTPlabeling of 3′-OH DNA ends and immunoperoxidase (1, 3), or byhematoxylin-eosin (HE) (2, 4). 1. Prominent nuclear DNA fragmentationdetected by AptoTag staining in serum-starved Survivin antisensetransfectants; 2. HE staining of antisense transfectants reveals thepresence of numerous apoptotic bodies (arrows); 3. AptoTag staining ofvector control HeLa cells detects a few sparse apoptotic cell (arrow);4. HE staining of vector control HeLa cells. The arrow indicates asingle apoptotic body. Magnification ×400. C. Effect of Survivin on cellgrowth. Twenty thousands vector control HeLa cells (Vector) or Survivinantisense transfectants (Antisense) were seeded in 24-well plates,induced with ZnSO₄, harvested at the indicated time points, and cellproliferation was determined microscopically by direct cell count. Dataare the mean SEM of replicates of a representative experiment out ofseven independent determinations.

FIGS. 8A-D show the expression of Survivin in HL-60 cells. HL-60 cellswere examined via Western and Northern blots for Survivin expression.

FIG. 9 presents a structural analysis of Survivin. The Survivin proteinwas analyzed using the Chou-Fasman, Garnier-Robson, Kyle-Doolittle,Eisenberg, Karplus-Schultz, Jameson-Wolf and Emini analysis methods.

FIGS. 10A-G show the nucleotide Sequence of Survivin, which correspondsto SEQ ID NO: 35. The amino acid sequence displayed in FIG. 10corresponds to SEQ ID NO: 34.

FIGS. 11A-C show the expression of Survivin and the generation andcharacterization of anti-Survivin mAb 8E2 by ELISA and immunoblotting.

FIG. 12 shows the site-directed mutagenesis of Survivin andidentification of key functional residues involved in apoptosisinhibition.

FIG. 13 shows the cytoprotective effect of Survivin addition onendothelial cell apoptosis.

FIGS. 14A-B show that the presence of Survivin is a negativepredictive-prognostic factor in neuroblastoma.

FIGS. 15A-B show that the presence of Survivin is a negative predictiveprognostic factor in high-grade non-Hodgkin's lymphoma.

FIG. 16 shows the down regulation of Survivin induced by inflammatoryand cytostatic cytokines.

FIG. 17 shows the effects of Survivin constructs or XIAP on apoptosisinduced in NIH3T3 cells by hydrogen peroxide.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

I. General Description

The present invention is based in part on identifying a novel proteinthat is expressed in tumor cells and inhibits cellular apoptosis,hereinafter the Survivin protein or Survivin. Survivin is also found tobe expressed in embryonic tissues.

The Survivin protein can be used as an agent, or serve as a target foragents, that can be used to inhibit or stimulate Survivin mediatedinhibition of cellular apoptosis, for example to block abnormal cellgrowth or to extend cell growth in culture.

As used herein, modulation of apoptosis means increasing or decreasingthe number of cells that would otherwise undergo apoptosis in a givencell population. This can be effected by increasing or decreasing theamount of Survivin present in a cell or by increasing or decreasing theactivity of the Survivin. Preferably, the given cell population in whichapoptosis is to be modulated is found in a tumor or other tissue orgroup of cells in which beneficial effect results from the modulation.Also, preferably, the increase or decrease in number of cells that wouldotherwise undergo apoptosis in a given cell population is at least about10%, 20%, 40% or more preferably at least about 50% of the cells in thatpopulation.

The present invention is further based on the development of methods forisolating proteins that bind to Survivin. Probes based on the Survivinprotein or fragments of Survivin as discussed below are used as captureprobes to isolate Survivin binding proteins. Dominant negative proteins,DNAs encoding these proteins, antibodies to these binding proteins,peptide fragments of these proteins or mimics of these proteins may beintroduced into cells to affect Survivin function. Additionally, theseproteins provide novel targets for screening of synthetic smallmolecules and combinatorial or naturally occurring compound libraries todiscover novel therapeutics to regulate Survivin function.

II. Identification, General Characterization and Tissue Distribution ofSurvivin

The present invention is based on the identification on chromosome 17q25of a novel member of the IAP family of inhibitors of apoptosis,designated Survivin, which may confer a selective advantage for cancercell growth. Relevant features of the Survivin gene include itsdevelopmentally- and differentiation-regulated expression, its nearlyidentical and complementary DNA sequence with the factor Xa receptorEPR-1, and its abundant in vivo expression in common human malignancies,but not in the adjacent non-neoplastic population. As described below,targeting Survivin expression by metallothionein-induction of EPR-1 mRNAresulted in apoptosis and inhibition of proliferation of HeLa celltransfectants.

In addition to their contribution to hemostasis, cellular receptors forblood proteases have recently emerged as pleiotropic signalingmolecules, playing a crucial role in embryologic development (Connolly,A. J. et al., Nature (1996) 381:516-519), and vasculogenesis (Carmeliet,P. et al., Nature (1996) 383:73-75). In this context, the Survivin genewas isolated by hybridization with the cDNA for EPR-1, a receptor forfactor Xa contributing to procoagulant activity (Altieri, D. C., FASEB J(1995) 9:860-865), and T cell activation (Duchosal, M. A. et al., Nature(1996) 380:352-356). Although the Survivin coding sequence was found tobe nearly identical to the EPR-1 cDNA, its orientation was unambiguouslyassigned to the antisense EPR-1 strand for the position of the consensussplice sites at intron-exon boundaries (Padgett, R. A. et al., Ann RevBiochem (1986) 55:1119-1150). On the other hand, the authenticity of theEPR-1 “sense” strand was demonstrated in previous studies, whenmammalian cells transfected with the EPR-1 cDNA or with chimeric EPR-1constructs (Ambrosini, G. et al., J Biol Chem (1996) 271:1243-1248 andAltieri, D. C., FASEB J (1995) 9:860-865), were recognized by anti-EPR-1mAbs and bound factor Xa in a specific and saturable reaction.

These findings could be reconciled by the existence of multiple, highlyhomologous, EPR-1 transcripts oriented in opposite directions. Theheterogeneity of EPR-1 mRNA and the complex pattern of Southernhybridization support this hypothesis. Previously, double strand EPR-1probes detected three strongly hybridizing bands of 1.9, 3.4 and ˜1.5 kbin mRNA of EPR-1⁺ cells (Altieri, D. C., FASEB J (1995) 9:860-865).Here, single strand-specific probes confirmed the presence of multiplemature and polyadenylated EPR-1-related messages, and revealed that the1.9 and 3.4 kb bands corresponded to two highly regulated, antisenseEPR-1 transcripts, while the 1.5 kb band, more accurately defined as 1.2kb, coincided with a genuine EPR-1-encoding message. While the 1.9 kbantisense transcript clearly originated from the Survivin gene describedhere, a gene encoding the 1.2 kb “sense” EPR-1 message has not yet beenidentified.

However, (i) the presence of several genomic EPR-1-hybridizing bandsunrelated to the Survivin gene, (ii) the different restriction patternof EPR-1 sequences in various species, and (iii) the numerous expressedsequence tag database entries matching (P=0.018-7×10⁻¹¹) the positive(accession n. W46267), or the negative (accession n. W34764, W83810,T29149) EPR-1 strand, altogether suggest the existence of at least asecond, highly-related, EPR-1 gene oriented in the opposite direction tothat described here, and encoding the previously characterized factor Xareceptor (Altieri, D. C., FASEB J (1995) 9:860-865).

A similar situation could arise from gene duplication event(s) involvingEPR-1 sequences. Interestingly, the single hybridization signal detectedon chromosome 17q25, and the single hybridizing bands identified in aSouthern blot of high molecular weight genomic DNA, suggest thatEPR-1-related sequences potentially oriented in opposite directions maybe adjacent in close proximity, within a physical interval of 75-130 kb.

The presence of multiple EPR-1 transcripts oriented in oppositedirections implies a reciprocal regulatory mechanism by naturallyoccurring antisense. This is consistent with the predominantlydiscordant and mutually exclusive distribution of sense and antisenseEPR-1 messages in developing or adult tissues in vivo, and during HL-60cell terminal differentiation. While antisense regulation is common inprokaryotes (Green, P. J. et al., Annu Rev Biochem (1986) 55:569-597), agrowing number of eukaryotic gene products have been recentlycharacterized for the occurrence of functional antisense transcriptspotentially participating in gene regulation, including basic fibroblastgrowth factor (Kimmelman, D. et al., Cell (1989) 59:687-696; Murphy, P.R. et al., Molecular Endocrinology (1994) 8:852-859), al(I) collagen(Farrell, C. M. et al., J Biol Chem (1995) 270:3400-3408 and Lukens,1995), n-myc (Krystal, G. W. et al., Mol Cell Biol (1990) 10:4180-4191),c-myc (Celano, P. et al., J Biol Chem (1992) 267:15092-15096), p53(Khochbin, S. et al., EMBO J (1989) 8:4107-4114), c-erbAa (Lazar, M. A.et al., Mol Cell Biol (1989) 9:1128-1136), and CD3 ζ/η/θ locus (Lerner,A. et al., J Immunol (1993) 151:3152-3162).

As described below, the existence of a EPR-1/Survivin gene balanceregulated by functional antisense was demonstrated in HeLa celltransfectants, when metallothionein-induced transcription of the EPR-1“sense” strand suppressed the expression of Survivin and profoundlyinfluenced apoptosis/cell proliferation (see below). This regulatorymechanism was not due to a potential protein association between EPR-1and Survivin, since the EPR-1 construct used for these experimentslacked a translational initiation codon. Additional experiments haveevaluated the ability of a Survivin antisense to inhibit cell growth.This was done by transiently co-transfecting the Survivin antisense witha lacZ reported plasmid and making a determination of cell viabilityafter a 48-h transfection in β-galactosidase expressing cells. Theresults indicated that the viability of Survivin antisense transfectantswas <20% of control cells transfected with the empty vector. A controlantisense of ICAM-1 (intercellular adhesion molecule-1) similarlyco-transfected in HeLa cells was ineffective.

Survivin was found to be a small protein of 142 amino acids (˜16.5 kDa)with no amino acid sequence homology to EPR-1, and designated Survivinfor the presence of a BIR-homologous domain (Birnbaum, M. J. et al., JVirology (1994) 68:2521-2528; Clem, R. J. et al., Mol Cell Biol (1994)14:5212-5222) found in LAP inhibitors of apoptosis (Duckett, C. S. etal., EMBO J (1996) 15:2685-2694; Hay, B. A. et al., Cell (1995)83:1253-1262; Liston, P. et al., Nature (1996) 379:349-353; Rothe, M. etal., Cell (1995) 83:1243-1252; Roy, N. et al., Cell (1995) 80:167-178).Based on overall sequence conservation, the absence of a carboxyterminus RING finger and the presence of a single, partially conserved,BIR domain, Survivin is the most distantly related member of the IAPfamily, sharing the highest degree of similarity with NAIP (Roy, N. etal., Cell (1995) 80:167-178). Thus, unlike bcl-2 or other IAP proteins,Survivin is undetectable in adult tissues, but becomes prominentlyexpressed in all the most common human cancers of lung, colon, breast,pancreas, and prostate, and in ˜50% of high-grade non-Hodgkin'slymphomas, in vivo. Additionally, unlike other IAP proteins (Deveraux,Q. et al., Nature (1997) 388:300-304), Survivin does not bind caspasesin a cell-free system (Roy, N. et al., Blood (1997) 595:2645.

Consistent with the anti-apoptosis properties of IAP proteins in vitro(Duckett, C. S. et al., EMBO J (1996) 15:2685-2694; Liston, P. et al.,Nature (1996) 379:349-353), and in vivo (Hay, B. A. et al., Cell (1995)83:1253-1262), inhibition of Survivin expression by the EPR-1 transcript(which naturally is antisense to Survivin) resulted in increasedapoptosis, as determined by in situ internucleosomal DNA fragmentationin HeLa cell transfectants. The ability of a RING finger-less IAPprotein to counteract apoptosis is not without a precedent, asdemonstrated by the suppression of apoptosis mediated by NAIP (Liston,P. et al., Nature (1996) 379:349-353), and by the in vivogain-of-function of a Drosophila IAP protein following deletion of theRING finger (Hay, B. A. et al., Cell (1995) 83:1253-1262). Althoughanti-apoptosis genes are thought to play an indirect role in cellgrowth, by favoring the accumulation of oncogenic mutations(s) inaberrantly long-living cells (Reed, J. C., J Cell Biol (1994) 124:1-6),down-regulation of Survivin resulted in a profound inhibition of HeLacell proliferation. While this may derive from rapid disappearance ofHeLa cells expressing the highest levels of antisense transcripts byapoptosis, a similar decrease in tumor cell proliferation has beenreported in vivo after antisense inhibition of bcl-2 (Reed, J. C. etal., Proc Natl Acad Sci USA (1990) 87:3660-3664).

The possibility that IAP proteins may play a more general role in cellproliferation, not exclusively restricted to apoptosis inhibition, hasbeen proposed earlier. Rothe et al., have recently demonstrated that theamino terminus BIR in two IAP proteins (cIAPs) physically interacts withthe signal transducers associated with the 75 kDa TNF receptor (Rothe,M. et al., Cell (1995) 83:1243-1252), a molecule primarily implicated incell proliferation and survival rather than apoptotic signaling(Tartaglia, L. A. et al., Immunol Today (1992) 13:151-153). While it isnot known if Survivin is physically linked to signaling molecules(Rothe, M. et al., Cell (1995) 83:1243-1252), the structural divergenceof its BIR as compared with other LAP proteins (Duckett, C. S. et al.,EMBO J (1996) 15:2685-2694; Hay, B. A. et al., Cell (1995) 83:1253-1262;Liston, P. et al., Nature (1996) 379:349-353; Rothe, M. et al., Cell(1995) 83:1243-1252; Roy, N. et al., Cell (1995) 80:167-178), may conferspecificity for supramolecular interaction(s) potentially relevant toits particular mechanism of apoptosis inhibition/cell growth.

Dysregulation of programmed cell death (apoptosis) has recently emergedas a primary mechanism contributing to the pathogenesis of various humandiseases, including cancer (Steller, H., Science (1995) 267:1445-1449;Thompson, C. B., Science (1995) 267:1456-1462). While the impact ofanti-apoptosis gene(s) in neoplasia is highlighted by the role of bcl-2in follicular lymphoma (Korsmeyer, S. J., Blood (1992) 80:879-886), apotential distribution of IAP proteins in cancer had not been previouslyinvestigated. In this context, one of the most striking characteristicsof Survivin was its abundant expression in actively proliferatingtransformed cell lines, and in all the most common human malignancies oflung, colon, pancreas, and breast, in vivo, but not in thenon-neoplastic adjacent cell population. This distribution in multiplehuman cancers may signal a fundamental role of this molecule inapoptosis/cell proliferation mechanisms in neoplasia. By analogy withthe paradigm of bcl-2, over-expression of Survivin in cancer may lead toaberrantly prolonged cell viability (Veis, D. J. et al., Cell (1993)75:229-240), increased resistance to chemotherapy-induced apoptosis(Miyashita, T. et al., Blood (1993) 81:151-157), and, as suggested bythe in vitro studies reported above, in a direct advantage fortransformed cell proliferation.

On the other hand, for its presence in normal PBMC and benign breastadenomas, in vivo (unpublished observations), Survivin expression cannotbe interpreted per se as a marker of malignant transformation but mayreflect a more general, developmental- or cell type-specific response tocertain stimuli. This is consistent with the presence of Survivin duringnormal embryonic (our unpublished observations) and fetal development,and its rapid disappearance in growth-arrested cell types (i.e. vitaminD₃-treated HL-60), and terminally-differentiated tissues, in vivo. Atvariance with other LAP proteins which are constitutively found in adultmature tissues (Duckett, C. S. et al., EMBO J (1996) 15:2685-2694;Liston, P. et al., Nature (1996) 379:349-353; Rothe, M. et al., Cell(1995) 83:1243-1252), this pattern of expression is reminiscent of thedistribution of bcl-2 in fetal tissues (LeBrun, D. P. et al., Am JPathol (1993) 142:743-753), and its more restricted presence indifferentiated cells, correlating with susceptibility to apoptosis(Hockenbery, D. M. et al., Proc Natl Acad Sci USA (1991) 88:6961-6965).

In summary, these findings identify Survivin as a novel link between IAPproteins and cancer, in vivo. A key implication of the data presentedbelow is the possibility to balance the effect of this potentanti-apoptosis gene by manipulating a normal cell regulatory mechanism,centered on the expression of EPR-1 (Altieri, D. C., FASEB J (1995)9:860-865). Targeting Survivin may then remove a selective advantage fortransformed cell growth and be therapeutically beneficial to increasethe susceptibility of cancer cells to chemotherapy-induced apoptosis.Along the same line, identification of polymorphic markers andconstruction of extended aplotypes within and around the EPR-1/Survivinlocus may provide new insights on the population genetics ofsusceptibility to chemotherapy.

III. Specific Embodiments

A. Survivin Protein

The present invention provides isolated Survivin protein, as well asallelic variants of the Survivin protein, and conservative amino acidsubstitutions of the Survivin protein. As used herein, the Survivinprotein (or Survivin) refers to a protein that has the amino acidsequence of human Survivin depicted in FIG. 4. The term “Survivinprotein” also includes naturally occurring allelic variants of Survivin,naturally occurring proteins that have a slightly different amino acidsequence than that specifically recited above. Allelic variants, thoughpossessing a slightly different amino acid sequence than those recitedabove, will still have the requisite ability to inhibit cellularapoptosis.

As used herein, the Survivin family of proteins refers to Survivinproteins that have been isolated from organisms in addition to humans.The methods used to identify and isolate other members of the Survivinfamily of proteins are described below.

Survivin is a member of the IAP (inhibitory apoptosis proteins) familyof protein. However, Survivin is the first member of a unique subfamilyof IAP proteins that differ from other LAP proteins in significant ways.Despite homology and sequence conservation in the BIR module betweenSurvivin and other members of this gene family, there are importantstructural differences that are unique to members of the Survivin familyof proteins. First unlike any other LAP protein, Survivin has only oneBIR module (most of the other molecules have 2-3). Further, Survivindoes not contain a carboxy-terminal RING finger but has a predictedcoiled-coil instead. Only the Neuronal Apoptosis Inhibitory Protein(NAIP) in the IAP family lacks a RING finger, but does not contain acarboxy-terminus coiled coil. Finally there is no DNA sequencesimilarity between Survivin and other IAP proteins (PCR primers designedon Survivin are unlikely to detect other IAP proteins and vice-versa).

The Survivin proteins of the present invention are preferably inisolated from. As used herein, a protein is said to be isolated whenphysical, mechanical or chemical methods are employed to remove theSurvivin protein from cellular constituents that are normally associatedwith the Survivin protein. A skilled artisan can readily employ standardpurification methods to obtain an isolated Survivin protein.

The Survivin proteins of the present invention further includeconservative variants of the Survivin proteins herein described. As usedherein, a conservative variant refers to alterations in the amino acidsequence that do not adversely affect the ability of the Survivinprotein to bind to a Survivin binding partner and/or to inhibit cellularapoptosis. A substitution, insertion or deletion is said to adverselyaffect the Survivin protein when the altered sequence prevents theSurvivin protein from associating with a Survivin binding partner and/orprevents the Survivin protein from inhibiting cellular apoptosis. Forexample, the overall charge, structure or hydrophobic/hydrophilicproperties of Survivin can be altered without adversely affecting theactivity of Survivin. Accordingly, the amino acid sequence of Survivincan be altered, for example to render the peptide more hydrophobic orhydrophilic, without adversely affecting the activity of Survivin.

The allelic variants, the conservative substitution variants and themembers of the Survivin family of proteins, will have the ability toinhibit cellular apoptosis. Such proteins will ordinarily have an aminoacid sequence having at least about 75% amino acid sequence identitywith the human Survivin sequence, more preferably at least about 80%,even more preferably at least about 90%, and most preferably at leastabout 95%. Identity or homology with respect to such sequences isdefined herein as the percentage of amino acid residues in the candidatesequence that are identical with the known peptides, after aligning thesequences and introducing gaps, if necessary, to achieve the maximumpercent homology, and including any conservative substitutions as beinghomologous. N-terminal, C-terminal or internal extensions, deletions, orinsertions into the peptide sequence shall not be construed as affectinghomology.

Thus, the Survivin proteins of the present invention include moleculeshaving the amino acid sequences disclosed in FIG. 1; fragments thereofhaving a consecutive sequence of at least about 3, 5, 10 or 15 aminoacid residues of the Survivin protein; amino acid sequence variants ofsuch sequence wherein an amino acid residue has been inserted N- orC-terminal to, or within, the disclosed Survivin sequence; amino acidsequence variants of the disclosed Survivin sequence, or their fragmentsas defined above, that have been substituted by another residue.Contemplated variants further include those containing predeterminedmutations by, e.g., homologous recombination, site-directed or PCRmutagenesis, and the corresponding Survivin proteins of other animalspecies, including but not limited to rabbit, rat, murine, porcine,bovine, ovine, equine and non-human primate species, and the alleles orother naturally occurring variants of the Survivin family of proteins;and derivatives wherein the Survivin protein has been covalentlymodified by substitution, chemical, enzymatic, or other appropriatemeans with a moiety other than a naturally occurring amino acid (forexample a detectable moiety such as an enzyme or radioisotope). Therecombinant Survivin protein also can be used to solve the molecularstructure of Survivin by 2D-NMR, circular dichroism and X-raycrystallography, thus integrating the site-directed mutagenesis approachand the rational design of specific small molecule inhibitors.

As described below, members of the Survivin family of proteins can beused: 1) as a target to block Survivin mediated inhibition of cellularapoptosis, 2) to identify and isolate binding partners that bindSurvivin, 3) in methods to identify agents that block the association ofSurvivin with a Survivin binding partner, 4) as a target to assay forSurvivin mediated inhibition of cellular apoptosis, 5) as an agent toblock cellular apoptosis, administered alone or as part of a combinationtherapy, 6) as a binding partner in an assay to quantitate circulatinglevels of anti-Survivin antibodies, 7) as an antigen to elicitproduction of anti-Survivin antibodies that in turn can be used in anassay to quantitate circulating levels of Survivin and or can be usedfor immunohistochemical purposes, and 8) as a therapeutic anti-cancervaccine, or component of a polyvalent vaccine.

B. Anti-Survivin Antibodies

The present invention further provides antibodies that selectively bindto a Survivin protein. The anti-Survivin antibodies particularlycontemplated include monoclonal and polyclonal antibodies as well asfragments containing the antigen binding domain and/or one or morecomplement determining regions.

Antibodies are generally prepared by immunizing a suitable mammalianhost using a Survivin protein, or fragment, in isolated orimmunoconjugated form (Harlow, Antibodies, Cold Spring Harbor Press, NY(1989)). FIG. 9 provides a Jameson-Wolf plot of the antigenic index ofvarious regions of Survivin. Such regions, in combination with the otherstructural analysis provided in FIG. 9, provide suitable fragments foruse in generating Survivin specific antibodies. Methods for preparingimmunogenic conjugates of a protein with a carrier such as BSA, KLH, orother carrier proteins are well known in the art. In some circumstances,direct conjugation using, for example, carbodiimide reagents may beused; in other instances linking reagents such as those supplied byPierce Chemical Co., Rockford, Ill., may be effective.

Administration of the Survivin immunogen is conducted generally byinjection over a suitable time period and with use of a suitableadjuvant, as is generally understood in the art. During the immunizationschedule, titers of antibodies can be taken to determine adequacy ofantibody formation.

While the polyclonal antisera produced in this way may be satisfactoryfor some applications, for pharmaceutical compositions, monoclonalantibody preparations are preferred. Immortalized cell lines whichsecrete a desired monoclonal antibody may be prepared using the standardmethod of Kohler and Milstein or modifications which effectimmortalization of lymphocytes or spleen cells, as is generally known.The immortalized cell lines secreting the desired antibodies arescreened by immunoassay in which the antigen is the Survivin peptide.When the appropriate immortalized cell culture secreting the desiredantibody is identified, the cells can be cultured either in vitro or byproduction in ascites fluid.

The desired monoclonal antibodies are then recovered from the culturesupernatant or from the ascites supernatant. Fragments of themonoclonals or the polyclonal antisera which contain the immunologicallysignificant portion can be used as antagonists, as well as the intactantibodies. Use of immunologically reactive fragments, such as the Fab,Fab′, of F(ab′)₂ fragments is often preferable, especially in atherapeutic context, as these fragments are generally less immunogenicthan the whole immunoglobulin.

The antibodies or fragments may also be produced, using currenttechnology, by recombinant means. Regions that bind specifically to thedesired regions of receptor can also be produced in the context ofchimeras or CDR grafted antibodies of multiple species origin.

The antibodies thus produced are useful not only as modulators of theassociation of Survivin with a Survivin binding partner, but are alsouseful in immunoassays for detecting Survivin expression/activity andfor the purification of Survivin and associated binding partners.

C. Survivin Encoding Nucleic Acid Molecules

The present invention further provides nucleic acid molecules thatencode Survivin, and the related Survivin proteins herein described,preferably in isolated form. For convenience, all Survivin encodingnucleic acid molecules will be referred to as the Survivin encodingnucleic acid molecule, the Survivin gene, or Survivin. As used herein,“nucleic acid” is defined as RNA or DNA that encodes a peptide asdefined above, or is complementary to a nucleic acid sequence encodingsuch peptides, or hybridizes to such a nucleic acid and remains stablybound to it under stringent conditions, or encodes a polypeptide sharingat least 75% sequence identity, preferably at least 80%, and morepreferably at least 85%, with the peptide sequences. Specificallycontemplated are genomic DNA, cDNA, mRNA and antisense molecules, aswell as nucleic acids based on an alternative backbone or includingalternative bases whether derived from natural sources or synthesized.Such hybridizing or complementary nucleic acid, however, is definedfurther as being novel and unobvious over any prior art nucleic acidincluding that which encodes, hybridizes under appropriate stringencyconditions, or is complementary to a nucleic acid encoding a Survivinprotein according to the present invention.

As used herein, “stringent conditions” are conditions in whichhybridization yields a clear and detectable sequence. Stringentconditions are those that (1) employ low ionic strength and hightemperature for washing, for example, NaCl, 0.0015 M sodium citrate,0.1% SDS at 50° C.; or (2) employ during hybridization a denaturingagent such as formamide, for example, 50% (vol/vol) formamide with 0.1%bovine serum albumin, 0.1% Ficoll, 0.1% polyvinylpyrrolidone, 50 mMsodium phosphate buffer at pH 6.5 with 750 mM NaCl, 75 mM sodium citrateat 42° C. Another example is use of 50% formamide, 5×SSC (0.75 M NaCl,0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodiumpyrophosphate, 5× Denhardt's solution, sonicated salmon sperm DNA (50μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42°C. in 0.2×SSC and 0.1% SDS. A skilled artisan can readily determine andvary the stringency conditions appropriately to obtain a clear anddetectable hybridization signal.

As used herein, a nucleic acid molecule is said to be “isolated” whenthe nucleic acid molecule is substantially separated from contaminantnucleic acid encoding other polypeptides from the source of nucleicacid.

The present invention further provides fragments of the Survivinencoding nucleic acid molecule. As used herein, a fragment of a Survivinencoding nucleic acid molecule refers to a small portion of the entireprotein encoding sequence. The size of the fragment will be determinedby the intended use. For example, if the fragment is chosen so as toencode an active portion of the Survivin protein, such as the C-terminalP coils or the IAP motif, the fragment will need to be large enough toencode the functional region(s) of the Survivin protein. If the fragmentis to be used as a nucleic acid probe or PCR primer, then the fragmentlength is chosen so as to obtain a relatively small number of falsepositives during probing/priming. FIG. 1 identifies fragments of theSurvivin gene that are particularly useful as selective hybridizationprobes or PCR primers.

Fragments of the Survivin encoding nucleic acid molecules of the presentinvention (i.e., synthetic oligonucleotides) that are used as probes orspecific primers for the polymerase chain reaction (PCR), or tosynthesize gene sequences encoding Survivin proteins can easily besynthesized by chemical techniques, for example, the phosphotriestermethod of Matteucci, et al., J Am Chem Soc (1981) 103:3185-3191 or usingautomated synthesis methods. In addition, larger DNA segments canreadily be prepared by well known methods, such as synthesis of a groupof oligonucleotides that define various modular segments of the Survivingene, followed by ligation of oligonucleotides to build the completemodified Survivin gene.

The Survivin encoding nucleic acid molecules of the present inventionmay further be modified so as to contain a detectable label fordiagnostic and probe purposes. As described above such probes can beused to identify other members of the Survivin family of proteins and asdescribed below, such probes can be used to detect Survivin expressionand tumor growth potential. A variety of such labels are known in theart and can readily be employed with the Survivin encoding moleculesherein described. Suitable labels include, but are not limited to,biotin, radiolabeled nucleotides and the like. A skilled artisan canemploy any of the art known labels to obtain a labeled Survivin encodingnucleic acid molecule.

Since the Survivin gene is an antisense or reverse orientation of theEPR-1 gene, particularly preferred are single-stranded probes for use indiagnostic purposes. Specifically, single-stranded diagnostic probes canbe used to selectively hybridize to mRNA that encodes Survivin.Single-stranded probes can be generated using known methods in which onestrand of a double-stranded probe is isolated or in which a singlestranded RNA probe is generated.

Modifications to the primary structure itself by deletion, addition, oralteration of the amino acids incorporated into the protein sequenceduring translation can be made without destroying the activity of theprotein. Such substitutions or other alterations result in proteinshaving an amino acid sequence encoded by DNA falling within thecontemplated scope of the present invention.

D. Isolation of Other Survivin Encoding Nucleic Acid Molecules

As described above, the identification of the human Survivin encodingnucleic acid molecule allows a skilled artisan to isolate nucleic acidmolecules that encode other members of the Survivin family of proteinsin addition to the human sequence herein described.

Essentially, a skilled artisan can readily use the amino acid sequenceof Survivin to generate antibody probes to screen expression librariesprepared from cells. Typically, polyclonal antiserum from mammals suchas rabbits immunized with the purified Survivin protein (as describedbelow) or monoclonal antibodies can be used to probe a mammalian cDNA orgenomic expression library, such as lambda gtll library, to obtain theappropriate coding sequence for Survivin, or other members of theSurvivin family of proteins. The cloned cDNA sequence can be expressedas a fusion protein, expressed directly using its own control sequences,or expressed by constructions using control sequences appropriate to theparticular host used for expression of the enzyme. FIG. 1 identifiesimportant antigenic and/or putative operative domains found in theSurvivin protein sequence. Such regions are preferred sources ofantigenic portions of the Survivin protein for the production of probe,diagnostic, and therapeutic antibodies.

Alternatively, a portion of the Survivin encoding sequence hereindescribed can be synthesized and used as a probe to retrieve DNAencoding a member of the Survivin family of proteins from any mammalianorganisms that contains such a protein. Oligomers containingapproximately 18-20 nucleotides (encoding about a 6-7 amino acidstretch) are prepared and used to screen genomic DNA or cDNA librariesto obtain hybridization under stringent conditions or conditions ofsufficient stringency to eliminate an undue level of false positives.

Additionally, pairs of oligonucleotide primers can be prepared for usein a polymerase chain reaction (PCR) to selectively clone aSurvivin-encoding nucleic acid molecule. A PCR denature/anneal/extendcycle for using such PCR primers is well known in the art and canreadily be adapted for use in isolating other Survivin encoding nucleicacid molecules. FIG. 1 identifies regions of the human Survivin genethat are particularly well suited for use as a probe or as primers.

E. rDNA Molecules Containing a Survivin Encoding Nucleic Acid Molecule

The present invention further provides recombinant DNA molecules (rDNAs)that contain a Survivin encoding sequence. As used herein, a rDNAmolecule is a DNA molecule that has been subjected to molecularmanipulation in vitro. Methods for generating rDNA molecules are wellknown in the art, for example, see Sambrook et al., Molecular Cloning(1989). In the preferred rDNA molecules, a Survivin encoding DNAsequence is operably linked to expression control sequences and/orvector sequences.

The choice of vector and/or expression control sequences to which one ofthe Survivin encoding sequences of the present invention is operablylinked depends directly, as is well known in the art, on the functionalproperties desired, e.g., protein expression, and the host cell to betransformed. A vector contemplated by the present invention is at leastcapable of directing the replication or insertion into the hostchromosome, and preferably also expression, of the Survivin geneincluded in the rDNA molecule.

Expression control elements that are used for regulating the expressionof an operably linked protein encoding sequence are known in the art andinclude, but are not limited to, inducible promoters, constitutivepromoters, secretion signals, and other regulatory elements. Preferably,the inducible promoter is readily controlled, such as being responsiveto a nutrient in the host cell's medium.

In one embodiment, the vector containing a Survivin encoding nucleicacid molecule will include a prokaryotic replicon, i.e., a DNA sequencehaving the ability to direct autonomous replication and maintenance ofthe recombinant DNA molecule extrachromosomally in a prokaryotic hostcell, such as a bacterial host cell, transformed therewith. Suchreplicons are well known in the art. In addition, vectors that include aprokaryotic replicon may also include a gene whose expression confers adetectable marker such as a drug resistance. Typical bacterial drugresistance genes are those that confer resistance to ampicillin ortetracycline.

Vectors that include a prokaryotic replicon can further include aprokaryotic or viral promoter capable of directing the expression(transcription and translation) of the Survivin encoding gene sequencesin a bacterial host cell, such as E. coli. A promoter is an expressioncontrol element formed by a DNA sequence that permits binding of RNApolymerase and transcription to occur. Promoter sequences compatiblewith bacterial hosts are typically provided in plasmid vectorscontaining convenient restriction sites for insertion of a DNA segmentof the present invention. Typical of such vector plasmids are pUC8,pUC9, pBR322 and pBR329 available from Biorad Laboratories, (Richmond,Calif.), pPL and pKK223 available from Pharmacia, Piscataway, N.J.

Expression vectors compatible with eukaryotic cells, preferably thosecompatible with vertebrate cells, can also be used to form rDNAmolecules that contain a Survivin encoding sequence. Eukaryotic cellexpression vectors are well known in the art and are available fromseveral commercial sources. Typically, such vectors are providedcontaining convenient restriction sites for insertion of the desired DNAsegment. Typical of such vectors are PSVL and pKSV-10 (Pharmacia),pBPV-1/pML2d (International Biotechnologies, Inc.), pTDT1 (ATCC,#31255), the vector pCDM8 described herein, and the like eukaryoticexpression vectors.

Eukaryotic cell expression vectors used to construct the rDNA moleculesof the present invention may further include a selectable marker that iseffective in an eukaryotic cell, preferably a drug resistance selectionmarker. A preferred drug resistance marker is the gene whose expressionresults in neomycin resistance, i.e., the neomycin phosphotransferase(neo) gene. Southern et al., J Mol Anal Genet (1982) 1:327-341.Alternatively, the selectable marker can be present on a separateplasmid, and the two vectors are introduced by co-transfection of thehost cell, and selected by culturing in the appropriate drug for theselectable marker.

F. Host Cells Containing an Exogenously Supplied Survivin EncodingNucleic Acid Molecule

The present invention further provides host cells transformed with anucleic acid molecule that encodes a Survivin protein of the presentinvention. The host cell can be either prokaryotic or eukaryotic.Eukaryotic cells useful for expression of a Survivin protein are notlimited, so long as the cell line is compatible with cell culturemethods and compatible with the propagation of the expression vector andexpression of the Survivin gene product. Preferred eukaryotic host cellsinclude, but are not limited to, yeast, insect and mammalian cells,preferably vertebrate cells such as those from a mouse, rat, monkey orhuman fibroblastic cell line, the most preferred being cells that do notnaturally express a Survivin protein. Preferred eukaryotic host cellsinclude the murine IL-3 dependent cell line BaF3, and the likeeukaryotic tissue culture cell lines.

Any prokaryotic host can be used to express a Survivin-encoding rDNAmolecule. The preferred prokaryotic host is E. coli.

Transformation of appropriate cell hosts with a rDNA molecule of thepresent invention is accomplished by well known methods that typicallydepend on the type of vector used and host system employed. With regardto transformation of prokaryotic host cells, electroporation and salttreatment methods are typically employed, see, for example, Cohen etal., Proc Natl Acad Sci USA (1972) 69:2110; and Maniatis et al.,Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory,Cold Spring Harbor, N.Y. (1982). With regard to transformation ofvertebrate cells with vectors containing rDNAs, electroporation,cationic lipid or salt treatment methods are typically employed, see,for example, Graham et al., Virol (1973) 52:456; Wigler et al., ProcNatl Acad Sci USA (1979) 76:1373-76.

Successfully transformed cells, i.e., cells that contain a rDNA moleculeof the present invention, can be identified by well known techniques.For example, cells resulting from the introduction of an rDNA of thepresent invention can be cloned to produce single colonies. Cells fromthose colonies can be harvested, lysed and their DNA content examinedfor the presence of the rDNA using a method such as that described bySouthern, J Mol Biol (1975) 98:503, or Berent et al., Biotech (1985)3:208 or the proteins produced from the cell assayed via animmunological method.

G. Production of Survivin Using a rDNA Molecule Encoding a SurvivinProtein

The present invention further provides methods for producing a Survivinprotein that uses one of the Survivin encoding nucleic acid moleculesherein described. In general terms, the production of a recombinant formof a Survivin protein typically involves the following steps.

First, a nucleic acid molecule is obtained that encodes a Survivinprotein, such as the nucleic acid molecule depicted in FIG. 1. If theSurvivin encoding sequence is uninterrupted by introns, it is directlysuitable for expression in any host. If not, then a spliced form of theSurvivin encoding nucleic acid molecule can be generated and used or theintron containing nucleic acid molecule can be used in a compatibleeukaryotic expression system.

The Survivin encoding nucleic acid molecule is then preferably placed inoperable linkage with suitable control sequences, as described above, toform an expression unit containing the Survivin encoding sequences. Theexpression unit is used to transform a suitable host and the transformedhost is cultured under conditions that allow the production of theSurvivin protein. Optionally the Survivin protein is isolated from themedium or from the cells; recovery and purification of the protein maynot be necessary in some instances where some impurities may betolerated.

Each of the foregoing steps can be done in a variety of ways. Forexample, the desired coding sequences may be obtained from genomicfragments and used directly in appropriate hosts. The construction ofexpression vectors that are operable in a variety of hosts isaccomplished using appropriate replicons and control sequences, as setforth above. The control sequences, expression vectors, andtransformation methods are dependent on the type of host cell used toexpress the gene and were discussed in detail earlier. Suitablerestriction sites can, if not normally available, be added to the endsof the coding sequence so as to provide an excisable gene to insert intothese vectors. A skilled artisan can readily adapt any host/expressionsystem known in the art for use with Survivin encoding sequences toproduce a Survivin protein.

H. Inhibition of Cell Death Using Survivin

As provided above, Survivin has been shown to inhibit cellularapoptosis. Accordingly, Survivin can be used in methods to extend thelife of cells. In general, cellular apoptosis can be inhibited bycontacting a cell with Survivin.

There are a number of situation in which it is desirable to inhibitcellular apoptosis. For example, the death of cells in tissues andorgans being prepared for transport and transplant can be inhibitedusing the Survivin protein. Alternatively, cells lines can beestablished for long term culture using Survivin encoding nucleic acidmolecules expressed in the cell line.

Hence, Survivin protein or Survivin gene expression can be used as ameans to inhibit cellular apoptosis. In cell culture systems, theSurvivin protein can be introduced into a cell, for example vialiposomal, Penetrin-1 delivery, or inclusion in the cell growth media,to inhibit apoptosis. Alternatively, the Survivin gene can be introducedand expressed in cells to increase the longevity of cells in culture.These provide means and methods for increasing the ability of culturedcells to produce desired compounds as well as provide methods ofestablishing long-term culture of primary explants of cells and tissues.

In tissue transplant, typically tissues and organs are stored andtransported prior to transplant. Cell death, by mechanisms similar toapoptosis, can lead to the loss of viability of the tissues or organs.In this setting, infusion with Survivin protein can be used as a methodto inhibit cell death in such tissues and organs.

There are pathological conditions characterized by premature andunwanted cellular apoptosis, for example in accelerated aging disorders.It is already known that inactivating mutations in a IAP protein maycause human diseases. The example is for the NAIP (see above). Studiesof patients with SMA (Spinal muscular atrophy, a neurodegenrativedisease that is thought to be caused by aberrantly increased apoptosis)has demonstrated that the NAIP gene is inactivated and deleted in 75% ofthese patients (Roy et al. 1995, Cell 80:167). By extension,inactivating mutations in Survivin can result in degenerative diseasescharacterized by aberrantly increased cell death. Haplotypic markerswithin and around the Survivin locus on chromosome 17q25 can be used instudies of population genetics to determine if that locus has alreadybeen implicated in diseases with increased apoptosis. In such cases, theSurvivin gene or the Survivin protein can be used to treat theconditions. Accordingly, the Survivin protein, or a Survivin encodingnucleic acid molecule is administered to an individual as a means oftreating abnormal apoptosis.

I. Methods to Identify Survivin Binding Partners

Another embodiment of the present invention provides methods for use inisolating and identifying binding partners of Survivin. Specifically,the Survivin protein can be used as a capture probe to identify Survivinbinding partners. As used herein, a Survivin binding partner is abiomolecule (such as a protein, DNA or other cofactor) that binds toSurvivin and mediates Survivin inhibition of cellular apoptosis.

In detail, a Survivin protein is mixed with an extract or fraction of acell that expresses Survivin under conditions that allow the associationof a binding partner with Survivin. After mixing, peptides that havebecome associated with Survivin are separated from the mixture. Thebinding partner that bound Survivin can then be removed and furtheranalyzed.

To identify and isolate a binding partner, the entire Survivin proteincan be used. Alternatively, a fragment of a Survivin protein can beused.

As used herein, a cellular extract refers to a preparation or fractionthat is made from a lysed or disrupted cell. The preferred source ofcellular extracts will be cells that naturally express Survivin.Examples of such cells include, but are not limited to tumor cells andembryonic tissues.

A variety of methods can be used to obtain an extract of a cell. Cellscan be disrupted using either physical or chemical disruption methods.Examples of physical disruption methods include, but are not limited to,sonication and mechanical shearing. Examples of chemical lysis methodsinclude, but are not limited to, detergent lysis and the enzyme lysis.In addition, the cellular extract can be prepared from cells that havebeen freshly isolated from a subject or from cells or cell lines whichhave been cultured. A skilled artisan can readily adapt methods forpreparing cellular extracts in order to obtain extracts for use in thepresent methods.

Once an extract of a cell is prepared, the extract is mixed with theSurvivin protein under conditions in which association of Survivin withthe binding partner can occur. A variety of conditions can be used, themost preferred being conditions that closely resemble conditions foundin the cytoplasm of a Survivin-expressing cell. Features such asosmolarity, pH, temperature, and the concentration of cellular extractused, can be varied to optimize the association of the Survivin with thebinding partner.

After mixing under appropriate conditions, Survivin is separated fromthe mixture. A variety of techniques can be utilized to separate themixture. For example, antibodies specific to Survivin can be used toimmunoprecipitate the Survivin and associated binding partner.Alternatively, standard chemical separation techniques such aschromatography and density/sediment centrifugation can be used.

After removal of nonassociated cellular constituents found in theextract, the binding partner can be dissociated from the Survivinprotein using conventional methods. For example, dissociation can beaccomplished by altering the salt concentration or pH of the mixture.

To aid in separating associated Survivin/binding partner pairs from themixed extract, the Survivin protein can be immobilized on a solidsupport. For example, Survivin can be attached to a nitrocellulosematrix or acrylic beads. Attachment of Survivin to a solid supportfurther aids in separating peptide/binding partner pair from otherconstituents found in the extract.

Alternatively, the Survivin-encoding nucleic acid molecule can be usedin a yeast two-hybrid system. The yeast two-hybrid system has been usedto identify other protein partner pairs and can readily be adapted toemploy the Survivin encoding molecules herein described.

J. Use of Survivin Binding Partners

Once isolated, the Survivin binding partners obtained using the abovedescribed methods can be used for a variety of purposes. The bindingpartners can be used to generate antibodies that bind to the Survivinbinding partner using techniques known in the art. Antibodies that binda Survivin binding partner can be used to assay Survivin activity, as atherapeutic agent to modulate a biological or pathological processmediated by Survivin, or to purify the binding partner. These uses aredescribed in detail below.

K. Methods to Identify Agents that Block Survivin/Binding PartnerInteractions

Another embodiment of the present invention provides methods foridentifying agents that reduce or block the association of Survivin witha Survivin binding partner. Specifically, Survivin is mixed with aSurvivin binding partner in the presence and absence of an agent to betested. After mixing under conditions that allow association of Survivinwith the Survivin binding partner, the two mixtures are analyzed andcompared to determine if the agent reduced or blocked the association ofSurvivin with the Survivin binding partner. Agents that block or reducethe association of Survivin with the Survivin binding partner will beidentified as decreasing the amount of association present in the samplecontaining the tested agent.

As used herein, an agent is said to reduce or block Survivin/Survivinbinding partner association when the presence of the agent decreases theextent to which or prevents the Survivin binding partner from becomingassociated with Survivin. One class of agents will reduce or block theassociation by binding to the Survivin binding partner while anotherclass of agents will reduce or block the association by binding toSurvivin.

The Survivin binding partner used in the above assay can either be anisolated and fully characterized protein or can be a partiallycharacterized protein that binds to Survivin or a Survivin bindingpartner that has been identified as being present in a cellular extract.It will be apparent to one of ordinary skill in the art that so long asthe Survivin binding partner has been characterized by an identifiableproperty, e.g., molecular weight, the present assay can be used.

Agents that are assayed in the above method can be randomly selected orrationally selected or designed. As used herein, an agent is said to berandomly selected when the agent is chosen randomly without consideringthe specific sequences involved in the association of the Survivin withthe Survivin binding partner. An example of randomly selected agents isthe use a chemical library or a peptide combinatorial library, or agrowth broth of an organism.

As used herein, an agent is said to be rationally selected or designedwhen the agent is chosen on a nonrandom basis which takes into accountthe sequence of the target site and/or its conformation in connectionwith the agent's action. As described above, there are two sites ofaction for agents that block Survivin/Survivin binding partnerinteraction: the binding partner contact site on Survivin and theSurvivin contact site on the Survivin binding partner. Agents can berationally selected or rationally designed by utilizing the peptidesequences that make up the contact sites of the Survivin/Survivinbinding partner pair. For example, a rationally selected peptide agentcan be a peptide whose amino acid sequence is identical to the Survivincontact site on the Survivin binding partner. Such an agent will reduceor block the association of Survivin with the binding partner by bindingto the Survivin binding partner.

The agents of the present invention can be, as examples, peptides, smallmolecules, vitamin derivatives, as well as carbohydrates. A skilledartisan can readily recognize that there is no limit as to thestructural nature of the agents of the present invention. One class ofagents of the present invention are peptide agents whose amino acidsequences are chosen based on the amino acid sequence of the Survivinprotein.

The peptide agents of the invention can be prepared using standard solidphase (or solution phase) peptide synthesis methods, as is known in theart. In addition, the DNA encoding these peptides may be synthesizedusing commercially available oligonucleotide synthesis instrumentationand produced recombinantly using standard recombinant productionsystems. The production using solid phase peptide synthesis isnecessitated if non-gene-encoded amino acids are to be included.

Another class of agents of the present invention are antibodiesimmunoreactive with critical positions of the Survivin or Survivinbinding partner. As described above, antibodies are obtained byimmunization of suitable mammalian subjects with peptides, containing asantigenic regions, those portions of the Survivin or binding partner,intended to be targeted by the antibodies. Critical regions include thecontact sites involved in the association of the Survivin with theSurvivin binding partner.

As discussed below, the important minimal sequence of residues involvedin Survivin activity define a functional linear domain that can beeffectively used as a bait for two-hybrid screening and identificationof potential Survivin-associated molecules. Use of such Survivinfragments will significantly increase the specificity of the screeningas opposed to using the full length molecule or the entire BIR domainand is therefore preferred. Similarly, this linear sequence can be alsoused as an affinity matrix also to isolate Survivin binding proteinsusing a biochemical affinity purification strategy.

L. Uses for Agents that Block the Association of Survivin with aSurvivin Binding Partner

As provided in the Background section, Survivin inhibits cellularapoptosis. Agents that reduce or block the interactions of Survivin witha Survivin binding partner can be used to modulate biological andpathologic processes associated with Survivin function and activity.

In detail, a biological or pathological process mediated by Survivin canbe modulated by administering to a subject an agent that blocks theinteraction of Survivin with a Survivin binding partner.

As used herein, a subject can be any mammal, so long as the mammal is inneed of modulation of a pathological or biological process mediated bySurvivin. The term “mammal” is meant an individual belonging to theclass Mammalia. The invention is particularly useful in the treatment ofhuman subjects.

As used herein, a biological or pathological process mediated bySurvivin or Survivin binding to a Survivin binding partner refers to thewide variety of cellular events mediated by Survivin. Pathologicalprocesses refer to a category of biological processes which produce adeleterious effect. For example, a pathological process mediated bySurvivin is the inhibition of cellular apoptosis in tumor cells. Thispathological process can be modulated using agents that reduce or blockSurvivin/Survivin binding partner association or block Survivinexpression.

As used herein, an agent is said to modulate a pathological process whenthe agent reduces the degree or severity of the process. For example, anagent is said to modulate tumor cell proliferation when the agentdecrease the rate or extent of cell division.

M. Administration of Survivin or Agents that Affect Survivin Activity

The agents of the present invention, whether they be agents that blockSurvivin/binding partner association or the Survivin protein, can beadministered via parenteral, subcutaneous, intravenous, intramuscular,intraperitoneal, transdermal, or buccal routes. Alternatively, orconcurrently, administration may be by the oral route. The dosageadministered will be dependent upon the age, health, and weight of therecipient, kind of concurrent treatment, if any, frequency of treatment,and the nature of the effect desired. For example, to treat tumor cellsas a means of blocking Survivin inhibition of apoptosis, an agent thatblocks Survivin expression or the interaction of Survivin with a bindingpartner, is administered systemically or locally to the individual beingtreated. As described below, there are many methods that can readily beadapted to administer such agents.

The present invention further provides compositions containing Survivinor one or more agents that block Survivin/binding partner association.While individual needs vary, a determination of optimal ranges ofeffective amounts of each component is within the skill of the art.Typical dosages comprise 0.1 to 100 μg/kg body wt. The preferred dosagescomprise 0.1 to 10 μg/kg body wt. The most preferred dosages comprise0.1 to 1 μg/kg body wt.

In addition to the pharmacologically active agent, the compositions ofthe present invention may contain suitable pharmaceutically acceptablecarriers comprising excipients and auxiliaries which facilitateprocessing of the active compounds into preparations which can be usedpharmaceutically for delivery to the site of action. Suitableformulations for parenteral administration include aqueous solutions ofthe active compounds in water-soluble form, for example, water-solublesalts. In addition, suspensions of the active compounds as appropriateoily injection suspensions may be administered. Suitable lipophilicsolvents or vehicles include fatty oils, for example, sesame oil, orsynthetic fatty acid esters, for example, ethyl oleate or triglycerides.Aqueous injection suspensions may contain substances which increase theviscosity of the suspension include, for example, sodium carboxymethylcellulose, sorbitol, and/or dextran. Optionally, the suspension may alsocontain stabilizers. Liposomes can also be used to encapsulate the agentfor delivery into the cell.

The pharmaceutical formulation for systemic administration according tothe invention may be formulated for enteral, parenteral or topicaladministration. Indeed, all three types of formulations may be usedsimultaneously to achieve systemic administration of the activeingredient.

Suitable formulations for oral administration include hard or softgelatin capsules, pills, tablets, including coated tablets, elixirs,suspensions, syrups or inhalations and controlled release forms thereof.

In practicing the methods of this invention, the compounds of thisinvention may be used alone or in combination, or in combination withother therapeutic or diagnostic agents. In certain preferredembodiments, the compounds of this invention may be coadministered alongwith other compounds typically prescribed for these conditions accordingto generally accepted medical practice, such as chemotherapeutic agents.

N. Combination Therapy

Survivin, as well as agents of the present invention that modulateSurvivin activity, can be provided alone, or in combination with anotheragents that modulate a particular biological or pathological process.For example, an agent of the present invention that reduces Survivininhibited apoptosis can be administered in combination with otheranti-cancer agents in methods to control cancer cell growth.Alternatively, Survivin can be administered with other protective agentsas a means for reducing cellular apoptosis. As used herein, two agentsare said to be administered in combination when the two agents areadministered simultaneously or are administered independently in afashion such that the agents will act at the same time.

Inhibition of Survivin activity/expression can be used in combinationwith conventional chemotherapies. The timing for using achemotherapeutic agent in combination with inhibiting Suvivinactivity/expression depends upon chemotherapeutic agent used and thetumor cell type treated. Examples of chemotherapeutic agents that can beused in combination with agents the effect Survivin activity/expression,includes, but is not limited to alkylating agents, such ascyclophosphamide (CTX; cytoxan), chlorambucil (CHL; leukeran), cisplatin(CisP; platinol) busulfan (myleran), melphalan, carmustine (BCNU),streptozotocin, triethylenemelamine (TEM), mitomycin C, and the likealkylating agents; anti-metabolites, such as methotrexate (MTX),etoposide (VP16; vepesid) 6-mercaptopurine (6 MP), 6-thioguanine (6TG),cytarabine (Ara-C), 5-fluorouracil (5FU), dacarbazine (DTIC), and thelike anti-metabolites; antibiotics, such as actinomycin D, doxorubicin(DXR; adriamycin), daunorubicin (daunomycin), bleomycin, mithramycin andthe like antibiotics; alkaloids, such as vinca alkaloids such asvincristine (VCR), vinblastine, and the like; and other antitumoragents, such as taxol and taxol derivatives, the cytostatic agentsglucocorticoids such as dexamethasone (DEX; decadron) andcorticosteroids such as prednisone, nucleoside enzyme inhibitors such ashydroxyurea, amino acid depleting enzymes such as asparaginase, and thelike diverse antitumor agents.

The use of the cytotoxic agents described above in chemotherapeuticregimens is generally well characterized in the cancer therapy arts, andtheir use herein falls under the same considerations for monitoringtolerance and effectiveness and for controlling administration routesand dosages, with some adjustments. For example, the actual dosages ofthe cytotoxic agents may vary depending upon the patient's cultured cellresponse determined by using the present histoculture methods.Generally, the dosage will be reduced compared to the amount used in theabsence of agents the effect Suvivin activity/expression.

Typical dosages of an effective cytotoxic agent can be in the rangesrecommended by the manufacturer, and where indicated by in vitroresponses or responses in animal models, can be reduced by up to aboutone order of magnitude concentration or amount. Thus, the actual dosagewill depend upon the judgment of the physician, the condition of thepatient, and the effectiveness of the therapeutic method based on the invitro responsiveness of the primary cultured malignant cells orhistocultured tissue sample, or the responses observed in theappropriate animal models.

O. Methods for Identifying Survivin Expression and Survivin-MediatedInhibition of Apoptosis

The present invention further provides methods for identifying cellsinvolved in Survivin-mediated inhibition of apoptosis as well astechniques that can be applied to diagnose biological and pathologicalprocesses associated with Survivin activity, the progression of suchconditions, the susceptibility of such conditions to treatment and theeffectiveness of treatment for such conditions. Specifically,Survivin-mediated inhibition of apoptosis can be identified bydetermining whether the Survivin protein is expressed in a cell. Cellsexpressing Survivin are considered to be inhibited from natural cellularapoptosis.

A variety of immunological and nucleic acid techniques can be used todetermine if the Survivin protein, or a Survivin encoding mRNA, isproduced in a particular cell. In one example, an extract of cells isprepared. The extract is then assayed to determine whether Survivin isexpressed in the cell. The degree of expression provides a measurementof the degree of inhibition of apoptosis. An increase in expression is ameasurement of an increased inhibition of apoptosis.

The measurement of Survivin expression can be used as a marker for avariety of purposes. In tumors, the present of Survivin expressioncorrelates with the proliferative potential of the tumor. In theExamples, it is shown that lymphomas display varying levels of Survivinexpression; lymphomas showing little to no Survivin expression are lowgrade lymphomas that can be effectively treated while lymphomas showinghigh levels of Survivin expression are high grade aggressive lymphomasthat typically cannot be effectively treated. Accordingly, the level ofSurvivin expression in a lymphoma, or other tumor, can be used as apredictive measurement of the aggressiveness and treatability of thetumor: the higher the level of Survivin expression, the higher theaggressiveness of the tumor and the more difficult the treatment willbe.

For example, to determine a tumor's proliferative potential oreasy/prognosis of treatment, an extract is made of the tumor cells andthe extract is then analyzed, for example, by gel electrophoresis, todetermine whether a Survivin protein is present. The presence and levelof Survivin correlates with the proliferative potential of the cancerand the ease of treatment. Alternatively, as described above,single-strand probes can be used to identify Survivin-encoding mRNA inthe cellular extracts.

In addition to being a marker of tumor aggressiveness and treatmentpotential, Survivin expression can be used as a measurement of theeffectiveness of anti-tumor therapy. In the Examples, it is shown thatHL-60, a promyelocytic cell line, had high levels of Survivinexpression. Treatment of HL-60 cells with retenoic acid, and anti-canceragent that acts by causing the differentiation of tumor cells, resultedin a reduction and elimination of Survivin expression. The reduction inexpression correlated with the degree of differentiation, the greaterthe differentiation, the lower the level of Survivin expression.Accordingly, Survivin expression can be used to measure theeffectiveness of anti-tumor treatment: if Survivin expression decreasesduring treatment, the treatment protocol is effective and can becontinued, whereas if Survivin expression remains unaltered, a differenttherapeutic regime or protocol needs to be performed

P. Other Methods to Control Survivin Expression

The present invention further provides additional methods that can beused to control Survivin expression in a cell. As discussed above andbelow, the Survivin promoter has a CPG island upstream from itspromoter. CPG islands are known targets for DNA methylation. The DNAmethylation sites in the CPG island serves as a means for regulatingSurvivin expression: methylation of CPG islands results in thesuppression of transcription of the gene found downstream from thepromoter. Accordingly, agents that methylate DNA, such as DNA methylase,and agents that stimulate the production of endogenous methylases, canbe used to control Survivin expression. Specifically, Survivinexpression in a cell can be reduced or eliminated by causing the cell toincrease the level of DNA methylation, particularly at the CPG islandfound upstream from the Survivin gene.

In another method, Survivin expression can be reduced by increasing thelevel of EPR-1 expression. As shown in the Examples, Survivin expressionand EPR-1 expression are generally mutually exclusive, expression ofEPR-1 results in a decrease or elimination of Survivin expression andvisa-a-versa. Accordingly, Survivin expression can be reduced by causinga cell to increase EPR-1 expression.

Q. Animal Models

We have isolated almost the complete structure of the mouse Survivingene. The gene is very conserved with its human counterpart includingsizes of introns, exons and intron-exon boundaries. The coding regionsof the mouse Survivin gene are 88%, to the extent sequenced, identicalto the human protein, thereby demonstrating strong evolutionaryconservation. We have also determined the differential anddevelopmentally-regulated distribution of Survivin during both human andmouse development. The availability of the complete structure of themouse Survivin gene and protein will allow the preparation of targetingvectors for gene knockout experiments and a more rational approach forthe generation of transgenic mice expressing Survivin under the controlof tissue-specific promoters.

The Survivin gene and the Survivin protein can serve as a target forgene therapy in a variety of contexts. For example, in one application,Survivin-deficient non-human animals can be generated using standardknock-out procedures to inactivate a Survivin gene or, if such animalsare non-viable, inducible Survivin antisense molecules can be used toregulate Survivin activity/expression. Alternatively, an animal can bealtered so as to contain a Survivin or antisense-Survivin expressionunit that directs the expression of Survivin or the antisense moleculein a tissue specific fashion. In such a uses, a non-human mammal, forexample a mouse or a rat, is generated in which the expression of theSurvivin gene is altered by inactivated or activation. This can beaccomplished using a variety of art-known procedures such as targetedrecombination. Once generated, the Survivin-deficient animal, the animalthat expresses Survivin in a tissue specific manner, or an animal thatexpresses an antisense molecule can be used to 1) identify biologicaland pathological processes mediated by Survivin, 2) identify proteinsand other genes that interact with Survivin, 3) identify agents that canbe exogenously supplied to overcome Survivin deficiency and 4) serve asan appropriate screen for identifying mutations within Survivin thatincrease or decrease activity.

For example, it is possible to generate transgenic mice expressing thehuman minigene for Survivin in a tissue specific-fashion and test theeffect of over-expression of the protein in district that normally donot contain Survivin. This strategy has been successfully used foranother family of apoptosis inhibitors, namely bcl-2 (Veis et al., Cell(1993) 75:229). Such an approach can readily be applied to the Survivinprotein and can be used to address the issue of a potential beneficialeffect of Survivin in a specific tissue area to protect cells fromapoptosis (transplant).

R. Survivin Gene Therapy

In another embodiment, genetic therapy can be used as a means formodulating a Survivin-mediated biological or pathological processes. Forexample, in tumor therapy, it may be desirable to introduce into thesubject being treated a genetic expression unit that encodes a modulatorof Survivin expression, such as an antisense encoding nucleic acidmolecule. Such a modulator can either be constitutively produced orinducible within a cell or specific target cell. This allows a continualor inducible supply of a modulator of Survivin expression within thesubject. Blocking Survivin expression allows for the control of tumorcell growth. Similarly, cells may be genetically engineered to expressSurvivin, e.g., in allograft pancreatic β cells for transplantation.

The level of Survivin gene expression may correlate with the level ofresistance to apoptosis. Thus, Survivin genes also find use inanti-apoptosis gene therapy. In particular, a functional Survivin genemay be used to sustain neuronal cells that undergo apoptosis in thecourse of a neurodegenerative disease, lymphocytes (i.e., T cells and Bcells), or cells that have been injured by ischemia.

Retroviral vectors, adenoviral vectors, adeno-associated viral vectors,or other viral vectors with the appropriate tropism for cells likely tobe involved in apoptosis (for example, epithelial cells) may be used asa gene transfer delivery system for a therapeutic Survivin geneconstruct. Numerous vectors useful for this purpose are generally known(Miller, Human Gene Therapy 15-14, 1990; Friedman, Science244:1275-1281, 1989; Eglitis and Anderson, BioTechniques 6:608-614,1988; Tolstoshev and Anderson, current opinion in biotechnology 1:55-61,1990; Sharp, The Lancet 337:1277-1278, 1991; Cornetta et al., NucleicAcid Research and Molecular Biology 36:311-322, 1987; Anderson, Science226:401-409, 1984; Moen, blood Cells 17:407-416, 1991; Miller et al.,Biotechniques 7:980-990, 1989; Le Gal La Salle et al., Science259:988-990, 1993; and Johnson, Chest 107:77S-83S, 1995). Retroviralvectors are particularly well developed and have been used in clinicalsettings (Rosenberg et al., N. Engl. J. Med 323:370, 1990; Anderson etal., U.S. Pat. No. 5,399,346).

Non-viral approaches may also be employed for the introduction oftherapeutic DNA into cells otherwise predicted to undergo apoptosis. Forexample, Survivin may be introduced into a neuron or a T cell bylipofection (Feigner et al., Proc. Natl. Acad. Sci. USA 84:7413, 1987;Ono et al., Neurosci. Lett. 117:259, 190; Brigham et al., Meth. Enz.101:512, 1983), asialorosonucoid-polylysine conjugation (Wu et al., J.Biol. Chem. 263:14621, 1988; Wu et al., J. Biol. Chem. 264:16985, 1989);or, less preferably, microinjection under surgical conditions (Wolff etal., Science 247:1465, 1990).

For any of the methods of application described above, the therapeuticSurvivin nucleic acid construct is preferably applied to the site of thepredicted apoptosis event (for example, by injection). However, it mayalso be applied to tissue in the vicinity of the predicted apoptosisevent or to a blood vessel supplying the cells predicted to undergoapoptosis.

In the constructs described, Survivin cDNA expression can be directedfrom any suitable promoter (e.g., the human cytomegalovirus (CMV),simian virus 40 (SV40), or metallothionein promoters), and regulated byany appropriate mammalian regulatory element. For example, if desired,enhancers known to preferentially direct gene expression in neuralcells, T cells, or B cells may be used to direct Survivin expression.The enhancers used could include, without limitation, those that arecharacterized as tissue- or cell-specific in their expression.Alternatively, if a Survivin genomic clone is used as a therapeuticconstruct (for example, following its isolation by hybridization withthe Survivin cDNA described above), regulation may be mediated by thecognate regulatory sequences or, if desired, by regulatory sequencesderived from a heterologous source, including any of the promoters orregulatory elements described above.

S. Use of the Survivin Promoter to Direct Gene Expression

The present invention further provides the promoter of the Survivin genein a form that can be used in generating expression vectors.Specifically, the Survivin promoter, identified as being 5′ from the ATGstart codon in of Survivin, can be used to direct the expression of anoperably linked protein encoding DNA sequence. Since the Survivinpromoter does not have a TATA box, a skilled artisan would use a 5′fragment, such as nucleotides 2560-2920 (including exon 1). The Survivinpromoter is expressed in fetal tissues and can therefore be used totarget protein expression in specific cell types during specific stagesof development. As discussed below, transfection of 3T3 cells with thec-myc oncogene results in the up-regulation of Survivin mRNA as detectedby Northern blots. Accordingly, DNA encoding anti-tumor polypeptidesunder the control of the Survivin promoter could be used to transfecttumor cell where they would be expressed. A skilled artisan can readilyuse the Survivin promoter in expression vectors using methods known inthe art.

T. Preventative Anti-Apoptotic Therapy

In a patient diagnosed to be heterozygous for a Survivin mutation or tobe susceptible to Survivin mutations (even if those mutations do not yetresult in alteration or loss of Survivin biological activity), or apatient diagnosed with a degenerative disease (e.g., motor neurondegenerative diseases such as SMA or ALS diseases), or diagnosed as HIVpositive, any of the disclosed therapies may be administered before theoccurrence of the disease phenotype. For example, the therapies may beprovided to a patient who is HIV positive but does not yet show adiminished T cell count or other overt signs of AIDS. In particular,compounds shown to increase Survivin expression or Survivin biologicalactivity may be administered by any standard dosage and route ofadministration. Alternatively, gene therapy using a Survivin expressionconstruct may be undertaken to reverse or prevent the cell defect priorto the development of the degenerative disease.

The methods of the instant invention may be used to reduce or diagnosethe disorders described herein in any mammal, for example, humans,domestics pets, or livestock. Where a non-human mammal is treated ordiagnosed, the Survivin polypeptide, nucleic acid, or antibody employedis preferably specific for that species.

U. Examples of Additional Apoptosis Assays

In addition to the foregoing discussion, specific examples of apoptosisassays are also provided in the following references. Assays forapoptosis in lymphocytes are disclosed by: Li et al., “Induction ofapoptosis in uninfected lymphocytes by HIV-1 Tat protein”, Science268:429-431, 1995; Gibellini et al., “Tat-expressing Jurkat cells showan increased resistance to different apoptotic stimuli, including acutehuman immunodeficiency virus-type 1 (HIV-1) infection”, Br. J. Haematol.89:24-33, 1995; Martin et al., “HIV-1 infection of human CD4+ T cells invitro. Differential induction of apoptosis in these cells.” J. Immunol.152:330-42, 1994; Terai et al., “Apoptosis as a mechanism of cell deathin cultured T lymphoblasts acutely infected with HIV-1”, J. Clin Invest.87:1710-5, 1991; Dhein et al., “Autocrine T-cell suicide mediated byAPO-1/(Fas/CD95)11, Nature 373:438-441, 1995; Katsikis et al., “Fasantigen stimulation induces marked apoptosis of T lymphocytes in humanimmunodeficiency virus-infected individuals”, J. Exp. Med.1815:2029-2036, 1995; Westendorp et al., Sensitization of T cells toCD95-mediated apoptosis by HIV-1 Tat and gp120”, Nature 375:497, 1995;DeRossi et al., Virology 198:234-44, 1994.

Assays for apoptosis in fibroblasts are disclosed by: Vossbeck et al.,“Direct transforming activity of TGF-beta on rat fibroblasts”, Int. J.Cancer 61:92-97, 1995; Goruppi et al., “Dissection of c-myc domainsinvolved in S phase induction of HIH3T3 fibroblasts”, Oncogene9:1537-44, 1994; Fernandez et al., “Differential sensitivity of normaland Ha-ras transformed C3H mouse embryo fibroblasts tumor necrosisfactor; induction of bcl-2, c-myc, and manganese superoxide dismutase inresistant cells”, Oncogene 9:2009-17, 1994; Harrington et al., “cMyc-induced apoptosis in fibroblasts is inhibited by specificcytokines”, EMBO J., 13:3286-3295, 1994; Itoh et al., “A novel proteindomain required for apoptosis. Mutational analysis of human Fasantigen”, J. Biol. Chem. 268:10932-7, 1993.

Assays for apoptosis in neuronal cells are disclosed by: Melino et al.,“Tissue transglutaminase and apoptosis: sense and antisense transfectionstudies with human neuroblastoma cells”, Mol. Cell Biol. 14:6584-6596,1994; Rosenblaum et al., “Evidence for hypoxia-induced, programmed celldeath of cultured neurons”, Ann. Neurol. 36:864-870, 1994; Sato et al.,“Neuronal differentiation of PC12 cells as a result of prevention ofcell death by bcl-2”, J. Neurobiol. 25:1227-1234, 1994; Ferrari et al.,“N-acetylcysteine D- and L-stereoisomers prevents apoptotic death ofneuronal cells”, J. Neurosci. 1516:2857-2866, 1995; Talley et al.,“Tumor necrosis factor alpha-induced apoptosis in human neuronal cells:protection by the antioxidant N-acetylcysteine and the genes bcl-2 andcrma”, Mol. Cell Biol. 1585:2359-2366, 1995; Talley et al., “TumorNecrosis Factor Alpha-Induced Apoptosis in Human Neuronal Cells:Protection by the Antioxidant N-Acetylcysteine and the Genes bcl-2 andcrma”, Mol. Cell. Biol. 15:2359-2366, 1995; Walkinshaw et al.,“Induction of apoptosis in catecholaminergic PC12 cells by L-DOPA.Implications for the treatment of Parkinson's disease,” J. Clin. Invest.95:2458-2464, 1995.

Assays for apoptosis in insect cells are disclosed by: Clem et al.,“Prevention of apoptosis by a baculovirus gene during infection oninsect cells”, Science 254:1388-90, 1991; Crook et al., “Anapoptosis-inhibiting baculovirus gene with a zinc finger-like motif”, J.Virol: 67:2168-74, 1993; Rabizadeh et al., “Expression of thebaculovirus p35 gene inhibits mammalian neural cell death”, J.Neurochem. 61:2318-21, 1993; Birnbaum et al., “An apoptosis inhibitinggene from a nuclear polyhedrosis virus encoding a polypeptide withCys/His sequence motifs”, J. Virol. 68:2521-8, 1994; Clem et al., Mol.Cell. Biol. 14:5212-5222, 1994.

V. Use of Survivin in Tissue and Organ Transplantation The presentinvention includes methods of inhibiting or preventing tissue or organtransplant rejection in a subject, comprising the local administrationof a Survivin polypeptide, Survivin polypeptide fragment, an apoptosisinhibiting peptidomimetic thereof, a transgene encoding a Survivinpolypeptide or a transgene encoding a Survivin polypeptide fragment tothe tissue, organ or to a site proximal to the transplant. Localdelivery of the polypeptides, peptidomimetics to the tissue, organ or toa site proximal to the transplant is accomplished by any means commonlyavailable, including but not limited to direct local perfusion,injection, microsponges, microcapsules, liposomes or time-releaseddelivery vehicles.

Local delivery of a transgene encoding a Survivin polypeptide or atransgene encoding a Survivin polypeptide fragment to the tissue, organor to a site proximal to the transplant may be accomplished with anyavailable vector, via lipofection or via direct plasmid DNA injection.See Qin et al. (1995) Transplantation 59(6): 809-816; Le Coultre et al.(1997) Eur. J. Pediatr. Surg. 7(4):221-226; Wang et al. (1992)Transplantation 53(3):703-705; Wang et al. (1996) Transpantation61(12):1726-1729; Schmid et al., (1997) Eur. J. Cardiothorac. Surg.11(6):1023-28; and Boasquevisque, C. et al. (1997) Ann. Thorac. Surg.63(6):1556-1561. Vectors encoding the transgene include both replicableand replication defective vectors, such as retroviral vectors,adenovirus vectors or other vectors with the appropriate tropism for thecells likely to be involved in apoptosis or cells proximal to the siteof apoptosis. In the transgene constructs, expression can be directedfrom any suitable promoter, including tissue specific promoters whichdirect gene expression in specific cell types, such as the human insulinpromoter. Local delivery of the transgene to the tissue, organ or to asite proximal to the transplant is accomplished by any means commonlyavailable, including but not limited to direct local perfusion,injection, microsponges, microcapsules, liposomes or time-releaseddelivery vehicles.

Without further description, it is believed that one of ordinary skillin the art can, using the preceding description and the followingillustrative examples, make and utilize the compounds of the presentinvention and practice the claimed methods. The following workingexamples therefore, specifically point out preferred embodiments of thepresent invention, and are not to be construed as limiting in any waythe remainder of the disclosure. Other generic configurations will beapparent to one skilled in the art. All journal articles and otherpublished documents such as patents and patent applications are herebyincorporated by reference in their entireties.

EXAMPLES Example 1 Experimental Procedures and Cloning

Cells and cell culture. The following cell lines were obtained fromAmerican Type Culture Collection (ATCC, Rockville, Md.), erythroleukemiaHEL, B-lymphoma Daudi and JY, monocytic THP-1, T leukemia Jurkat,epithelial carcinoma HeLa, promyelocytic HL-60, and non-transformedhuman lung fibroblast Lu18. The T leukemia cell line MOLT13 wascharacterized previously (Altieri, D. C., FASEB J (1995) 9:860-865).Cells were maintained in culture in complete medium RPMI 1640 or DMEM(HeLa, Lu18) (BioWhittaker, Walkersville, Md.), supplemented with 10%heat-inactivated fetal bovine serum (FBS, Whittaker), 2 mM L-glutamine,and 10 mM HEPES. Human umbilical vein endothelial cells (HUVEC) wereisolated by collagenase treatment and maintained in culture in DMEMmedium supplemented with 20% FBS, 2 mM L-glutamine and endothelial cellgrowth factor (Biomedical Technologies, Stoughton, Mass.).

Peripheral blood mononuclear cells (PBMC) were isolated from heparinizedblood collected from normal informed volunteers by differentialcentrifugation on Ficoll-Hypaque (Pharmacia, Piscataway, N.J.) at 400 gfor 22° C., and washed in phosphate buffered saline (PBS), pH 7.4. Insome experiments, HL-60 cells were terminally differentiated to a maturemonocytic phenotype by a 72 h culture in the presence of 0.1 μM 1,25-dihydroxy-vitamin D₃ and 17.8 μg/ml indomethacin (Sigma Chemical Co.,St. Louis, Mo.). De novo induction of differentiation-dependent markerson vitamin D₃-treated HL-60 cells, including CD11b/CD 18 integrin(Hickstein, D. D. et al., J Immunol (1987) 138:513-519) was determinedby flow cytometry with anti-CD11b mAb LM2/1.

Genomic and cDNA cloning, chromosomal localization and Southern blots. Ahuman P1 genomic library (Genome Systems, St. Louis, Mo.) was screenedby hybridization with a 1.6 kb fragment containing the complete humanEPR-1 cDNA (Altieri, D. C., FASEB J (1995) 9:860-865). Three overlappingclones were isolated, purified and confirmed by Southern hybridizationwith the EPR-1 cDNA. Hybridizing fragments generated by restrictiondigest with BamHI, HindIII and XbaI (Boehringer Mannheim, Indianapolis,Ind.) were cloned in pBluescript (pBSKS⁻, Stratagene, San Diego, Calif.)for further analysis. An overlapping contig spanning 14796 bp from twoEPR-1-hybridizing P1 clones was arrayed, characterized by restrictionanalysis, and completely sequenced on both strands by Taq FSpolymerase-based automated sequencing using a Applied BioSystem Prism377 automated sequencer (Foster City, Calif.). In some experiments, 10mg of total RNA extracted from HeLa cells by the guanidiniumisothiocyanate method was primed with EPR-1 forward “sense”oligonucleotide C3/27 (bp 80-102) and reverse transcribed in thepresence of 200 U of Superscript II (Life Science, Grand Island, N.Y.)for 50 min at 42 □C.

The resulting cDNA was amplified by PCR in the presence of 0.5 mg ofEPR-1-derived primers T5/27 (bp 161-184) and G11/16 (1124-1098,numbering from the EPR-1 coding sequence), 200 mM dNTPs (New EnglandBiolabs, Beverly, Mass.) and 2 U Vent DNA polymerase (New EnglandBiolabs) in a total volume of 50 ml. After 35 cycles of amplificationwith annealing at 58° C. for 1 min, denaturation at 94° C. for 1 min andextension at 72° C. for 1 min, the product was analyzed by agarose gelelectrophoresis, subcloned in pCRII (Invitrogen Corp., San Diego,Calif.), and completely sequenced on both strands. Contig assembly, andDNA and protein sequence analyses were performed using Lasergene(DNASTAR, Madison, Wis.) and MacVector (Eastman Kodak, Rochester, N.Y.)software packages. Chromosomal location of the EPR-1-hybridizing genewas carried out by fluorescence in situ hybridization. Purified DNA froma EPR-1-hybridizing P1 clone was labeled with digoxigenin dUTP (AmershamCorp., Arlington Heights, Ill.) by nick translation.

The labeled probe was combined with sheared human DNA and hybridized tonormal metaphase chromosomes derived from phytohemagglutinin-stimulatedPBMC in a solution containing 50% formamide, 10% dextran sulfate and2×SSC. For two-color staining, biotin-conjugated probe D17Z1, specificfor the centromere of chromosome 17, was co-hybridized with thedigoxigenin-labeled P1 clone. Specific staining was detected byincubating the hybridized slides with fluoresceinated anti-digoxigeninantibodies and Texas red avidin. Slides were counterstained withpropidium iodide for one color labeling, or with DAPI for two colorlabeling. A total of 80 metaphase cells were analyzed with 69 cellsexhibiting specific labeling. For Southern hybridization, human genomicDNA was extracted from HeLa cells according to published protocols,digested with EcoRI, BamHI, XbaI or HindIII, separated on a 0.8% agarosegel and transferred to GeneScreen nylon membranes (New England Nuclear,Boston, Mass.).

After UV cross-linking (Stratalinker, Stratagene, San Diego, Calif.),the membrane was prehybridized with 100 mg/ml of denatured salmon spermDNA (Promega Corp. Madison, Wis.) in 5×SSC, 0.5% SDS, 5× Denhardt'ssolution and 0.1% sodium pyrophosphate at 65° C. in a rollerhybridization oven (Hoefer Scientific, San Francisco, Calif.).Hybridization was carried out with gel-purified (GeneClean Bio101,Vista, Calif.), ³²P-dCTP (Amersham) random-primed labeled(Boehringer-Mannheim, Indianapolis, Ind.) 1.6 kb EPR-1 cDNA for 16 h at65° C.

After two washes in 2×SSC, 1% SDS for 30 min at 65° C., and 0.2×SSC at22° C., radioactive bands were visualized by autoradiography using aKodak X-Omat AR X-ray film and intensifying screens (DuPont de Nemours,Wilmington, Del.). In other experiments, cultured lymphoblastoid cellswere embedded in LMP agarose (Bio Rad, Richmond, Calif.) at theconcentration of 2×10⁶/220 μl block and DNA was extracted by standardprocedures. After block digestion with Mlul or NotI, samples wereseparated by pulsed field gel electrophoresis on a 1% agarose gel for 20h at 200 V with a pulse time of 75 sec using a Bio-Rad CHEF DRIIapparatus (Hercules, Calif.). After transfer to nylon membranes, and UVcross-linking, hybridization with the EPR-1 cDNA and washes were carriedout as described above.

In another series of experiments, a blot containing aliquots of genomicDNA isolated from several species (Clontech, San Francisco, Calif.) washybridized with a 3′ 548 bp fragment of the EPR-1 cDNA, as describedabove.

Northern blots. Single strand probes specific for sense or antisenseEPR-1 sequences were generated by asymmetric PCR amplification of a 301bp fragment of the EPR-1 cDNA. The template, comprising the first 5′ 226bp of the EPR-1 coding sequence plus 75 bp of the retained regulatoryintron (Altieri, D. C., FASEB J (1995) 9:860-865), was generated byrestriction digest of the EPR-1 cDNA with EcoRI (cloning site) andSacII, gel-purified, and mixed in a total volume of 10 ml with 15 pmoldNTP (New England Biolabs), 7.5 pmol dCTP, and 25 mCi ³²P-dCTP(Amersham), in the presence of 20 mM Tris HCl, 50 mM KCl, pH 8.4, 1.5 mMMgCl₂, and 2.5 U of Taq DNA polymerase (Life Science).

Generation of a EPR-1-specific antisense probe was carried out byaddition of 0.2 mg/ml of a “SacII” reverse oligonucleotide5′TGCTGGCCGCTCCTCCCTC3′ (SEQ ID NO: 1), while extension of the EPR-1positive strand and generation of a Survivin-specific probe wasperformed using 0.2 mg/ml of forward F11 oligonucleotide5′ATGACCTCCAGAGGTTTC3′ (SEQ ID NO: 2). Twenty-five cycles ofamplification were carried with denaturation at 94° C. for 1 min,annealing at 52° C. for 1 min, and extension at 72° C. for 1 min. TheEPR-1 sense or antisense probes were centrifuged through a Sephadex G-50spin column (Worthington Biochemical Corp., Freehold, N.J.) at 14,000 gfor 5 min to separate free from incorporated radioactivity, heated at100° C. for 2 min, and immediately added to the hybridization reaction.

Identical strand-specific probes were used for hybridization of multipletissue blots of adult or fetal human mRNA (Clontech), in 5×SSPE, 10×Denhardt's solution, 2% SDS, 100 mg/ml denatured salmon sperm DNA at 60°C. for 14 h, and washes at 60° C., as described above. Aliquots of totalRNA extracted from undifferentiated or vitamin D₃ terminallydifferentiated HL-60 cells, were processed for Northern hybridizationwith Survivin-specific single strand probe, as described above.

Example 2 Production of Anti-Survivin Antibodies

A Survivin sequence-specific antibody, called JC700, was produced andcharacterized as follows. A seventeenmer peptide corresponding to theSurvivin sequence A ³PTLPPAWQPFLKDHRI¹⁹ (SEQ ID NO: 3), was synthesizedand characterized by mass spectrometry. One hundred mg of the Survivinpeptide were coupled in a 1:1 ratio to Keyhole Limpet Hemocyanin andinjected s. c. into a rabbit in complete Freund's adjuvant. After a4-week interval, animals were boosted with s. c. injection of 100 mg ofpeptide in incomplete Freund's adjuvant and sequentially boosted andbled at alternate weeks.

Purification of the anti-Survivin antibody was carried out by affinitychromatography on a peptide-Sepharose matrix (5 mg/ml of peptide) withelution of the specific IgG fraction in 1 mM glycine, pH 2.5.Specificity of the affinity-purified anti-Survivin antibody, designatedJC700, was determined by ELISA against the immobilized Survivin peptideor a control EPR-1 peptide by absorbance at OD₄₀₅.

Example 3 Production of a Monoclonal Antibody Against a Survivin fusionProtein

The Survivin cDNA was expressed as a GST-fusion protein in E. Coli BL21strain and purified to homogeneity with removal of the GST frame. Thepurified protein was used to inject mice and generate monoclonalantibodies using standard hybridoma technology. Three independent mAbswere isolated, cloned twice by limiting dilution and furthercharacterized. One of the new anti-Survivin mAbs, designated 8E2,recognized the immobilized, purified recombinant Survivin by ELISA andbound to Survivin in immunoblots, as shown in FIG. 11.

Example 4 Immunoblotting and In Situ Hybridization

For immunoblotting, aliquots of SDS-solubilized extracts of varioustransformed cell lines, non-transformed HUVEC, PBMC or Lu18, orundifferentiated or vitamin D₃-differentiated HL-60 cells, werenormalized for protein content by absorbance at OD₂₈₀, separated byelectrophoresis on a 5-20% SDS polyacrylamide gradient gel under nonreducing conditions, and electroblotted to Immobilon membranes(Millipore Corp., New Bedford, Mass.) at 1.1 A for 30 min at 22° C. Themembrane was blocked in TBS, pH 7.4, plus 5% milk, and incubated with 20mg/ml of control non-immune rabbit IgG or anti-Survivin antibody JC700for 1 h at 22° C., followed by washes in TBS, pH 7.4, and addition of a1:7500 dilution of alkaline phosphatase-conjugated goat anti-rabbit IgG(Promega) for 30 min at 22° C. Binding of the primary antibody wasrevealed by addition of 75 mg/ml nitro blue tetrazolium in 70%dimethylformamide (Sigma Chemical Co., St. Louis, Mo.) plus 50 mg/ml5-bromo-4-chloro-3-indolyl phosphate (Sigma) in 100% dimethylformamide.

Tissue samples, immunohistochemistry and in situ hybridization. Tissuesamples from colon adenocarcinoma (6 cases), lung squamous cellcarcinoma (6 cases), lung adenocarcinoma (9 cases), pancreasadenocarcinoma (2 cases), invasive breast adenocarcinoma (7 cases), wereobtained from the archives of Yale-New Haven Hospital and used in thepresent study. Samples of 44 high grade lymphoma tissues and 7 low gradelymphoma tissue was also obtained. Tissue samples were fixed informalin, embedded in paraffin, cut in 5 μm sections, deparaffinized inxylene, and rehydrated in graded alcohol followed by quenching ofendogenous peroxidase activity by treatment with 2% H₂O₂ in methanol.

For immunostaining, the slides were boiled for 5 min in a standardpressure cooker, blocked in 10% normal goat serum, and incubated withaffinity-purified anti-Survivin antibody JC700 (20 μg/ml) for 14 h at 4°C. After washes in PBS, pH 7.4, slides were further incubated withbiotin-conjugated goat anti-rabbit IgG (Vector Laboratories, Burlingame,Calif.) for 30 min at 22 □C, and washed in PBS, pH 7.4. After additionof streptavidin-biotin conjugated peroxidase (Boehringer Mannheim) for30 min at 22° C., slides were washed, and binding of the primary mAbswas revealed by addition of 3′-3′-diamino-benzidine (DAB) andcounterstaining with hematoxylin.

Negative controls were carried out by replacing the primary antibodywith normal goat serum, under the same experimental conditions. In someexperiments, aliquots of JC700 antibody were pre-adsorbed with 25 mg/mlof the Survivin 3-19 peptide before tissue staining. For in situhybridization, 1 μg of the Survivin cDNA containing the entire codingsequence plus 271 bp of 3′ untranslated region in pcDNA3 (Invitrogen),was completely digested with EcoRI and transcribed in the antisenseorientation using T7 RNA polymerase in the presence of digoxigenin11-uridine-5′ triphosphate (Boehringer Mannheim). Tissue slides werecoated with 1% gelatin, 0.1% chrome-alum, baked at 120° C. for 2 h, andstored dust-free at 22° C. Sections were deparaffinized and rehydratedthrough graded alcohol, digested with proteinase K (1 μg/ml in 100 mMTris HCl pH 8.7, 50 mM EDTA) for 30 min at 37° C., and acetylated in0.25% acetic anhydride acid and 100 mM triethanolamine pH 8.0 for 10 minat 22° C.

Detection of Survivin mRNA in human tissues was carried out by in situhybridization of the Survivin antisense riboprobe in a buffer containing4×SSC, 1× Denhardt's solution, 50% deionized formamide, 250 μg/ml yeasttRNA, 500 μg/ml salmon sperm DNA and 5% dextran for 16 h at 50° C. Afterwashes in 2×SSC for 90 min at 48° C., immobilized digoxigenin wasdetected using an anti-digoxigenin mAb (Boehringer Mannheim) at a 1:3000dilution, and revealed by alkaline phosphatase staining with NBT/BCIPcytochemical stain.

Example 5 Expression of Survivin in Human Cancers

Survivin is prominently expressed in human cancer. For its abundantdistribution in transformed cell types, a potential expression ofSurvivin in neoplasia was investigated, in vivo. Immunohistochemicalanalysis of formalin-fixed, paraffin embedded tissue sections with theaffinity-purified anti-Survivin JC700 antibody demonstrated abundantexpression of Survivin in all cases examined of human lung cancer,including adenocarcinoma (FIG. 6A), and squamous cell carcinoma (FIG.6C). Consistent with the topography of other LAP proteins (Duckett, C.S. et al., EMBO J (1996) 15:2685-2694), expression of the protein wasexclusively localized to the cytoplasm of tumor cells, while theadjacent normal gland epithelium of the lung did not express Survivin(FIG. 6C, arrow). No staining was observed when the anti-Survivinantibody was substituted with control goat serum (not shown), or afterpre-adsorption with the immunizing Survivin 3-19 peptide (FIG. 6B), thusconfirming the specificity of the observed recognition.

Prominent accumulation of Survivin mRNA in squamous lung cell carcinomawas independently demonstrated by in situ hybridization with aSurvivin-specific single strand riboprobe (FIG. 6D). Survivin was alsoabundantly detected in all cases examined of adenocarcinoma of pancreas(FIG. 6E), and breast (not shown) by immunohistochemistry, and colon(FIG. 6G) by in situ hybridization. However, consistent with its absencein non-transformed cell types HUVEC and Lu18 (FIG. 4C), in maturetissues (FIG. 3), and in terminally-differentiated HL-60 cells (FIG. 5),no reactivity of the anti-Survivin JC700 antibody was observed withnormal exocrine pancreatic epithelial cells by immunohistochemistry(FIG. 6F), and no Survivin mRNA was found in the adjacent non-neoplasticcolon gland epithelium by in situ hybridization (FIG. 6H).

Expression of Survivin in Lymphoma Tissue. Tissue samples were obtainedfrom 44 patients with aggressive, high grade lymphoma and 7 samples wereobtained from 7 patients with non-aggressive, low grade lymphoma. Thesample were treated as described above and examined for Survivinexpression. None of the low grade lymphoma samples displayed Survivinexpression whereas 27 samples (61%) from patients with high gradelymphoma expressed Survivin.

Example 6 Expression of Survivin in Other Cancers

In addition to the malignant forms of cancer discussed above, theexpression of Survivin in other types of cancers was investigated in theinventors' laboratory or collaboratively with other academicinvestigators. Survivin was found prominently expressed in the mostaggressive and metastatic forms of malignant thymoma (−100 casestested), in head and-neck squamous cell carcinoma (−140 cases) and inall forms of prostate cancer (15 cases), including the transition lesionof benign prostate hyperplasia. The most aggressive forms ofneuroblastoma are also positive for Survivin as discussed below.

Example 7 Tissue Specific Expression of Survivin

Survivin, was recently found in all the most common human cancers butnot in normal, terminally differentiated adult tissues. The expressionof Survivin in embryonic and fetal development was investigated.Immunohistochemistry and in situ hybridization studies demonstratedstrong expression of Survivin in several apoptosis-regulated fetaltissues, including the stem cell layer of stratified epithelia,endocrine pancreas and thymic medulla, with a pattern non-overlappingwith that of another apoptosis inhibitor, i.e. bcl-2. Asequence-specific antibody to Survivin immunoblotted a single −16.5 kDSurvivin band in human fetal lung, liver, heart, kidney andgastrointestinal tract. In mouse embryo, prominent and nearly ubiquitousdistribution of Survivin was found at embryonic date (E) 11.5, whereasat E15-21, Survivin expression was restricted to the distal bronchiolarepithelium of the lung and neural crest-derived cells, including dorsalroot ganglion neurons, hypophysis and the chorioid plexus. These datasuggest that expression of Survivin in embryonic and fetal developmentmay contribute to tissue homeostasis and differentiation independentlyof bcl-2.

Example 8 Preparation of Survivin Transfectants

Inducible Survivin antisense transfectants and apoptosis/proliferationexperiments. A 708 bp SmaI-EcoRI fragment comprising nucleotides379-1087 of the EPR-1 cDNA, was directionally cloned in the senseorientation in the mammalian cell expression vector pML1 (generouslyprovided by Dr. R. Pytela, Cardiovascular Research Institute, Universityof California, San Francisco). The vector is derived from the episomalmammalian cell expression vector pCEP4 by replacing the cytomegaloviruspromoter cassette with the mMT1 promoter, directing Zn²⁺-dependentexpression of recombinant proteins in mammalian cells (Lukashev, M. E.et al., J Biol Chem (1994) 269:18311-18314).

Ten million HeLa cells were incubated with 10 mg of pML1 DNA containingthe Survivin antisense construct plus 50 mg of salmon sperm DNA for 15min on ice, followed by a single electric pulse delivered by a GenePulser apparatus (Bio-Rad) at 350 V at 960 μF. Forty-eight h aftertransfection, cells were diluted fifteen fold, plated onto 100 mmdiameter tissue culture dishes and selected for 4 weeks in completegrowth medium containing 0.4 mg/ml hygromycin. Apoptosis in controlcultures or Survivin antisense HeLa cell transfectants was evaluated byin situ detection of internucleosomal DNA degradation afterZn²⁺-dependent induction of EPR-1 transcription under serum-starvingconditions.

Briefly, control or antisense Survivin transfectants were treated with200 mM ZnSO₄ in 0% FBS for 24 h at 37° C. Cells were harvested,centrifuged at 800 g for 10 min at 4° C., and the pellet was fixed in10% formalin overnight, dehydrated, embedded in paraffin blocks, andsections of 3-5 mm were put on high adhesive slides. Samples weretreated with 20 mg/ml proteinase K for 15 min at 22° C., washed indistilled water, quenched of endogenous peroxidase in 2% H₂O₂ in PBS,and subsequently mixed with digoxigenin-labeled dUTP in the presence ofterminal deoxynucleotidyl transferase (TdT) followed by peroxidaseconjugated anti-digoxigenin antibody.

Nuclear staining in apoptotic cells was detected by DAB, according tothe manufacturer's instructions (AptoTag, Oncor, Gaithersburg, Md.).Control experiments were performed by omitting the enzyme incubationstep. Morphologic features of apoptotic cells (apoptotic bodies) underthe various conditions tested were detected by hematoxylin/eosinstaining of the same slides.

For proliferation experiments, vector control HeLa cells or Survivinantisense transfectants were plated at 20×10⁴/well onto 24-well tissueculture plates (Costar), induced with 200 mM ZnSO₄ for 16 h at 37° C.,harvested at 24 h intervals, and cell proliferation under the variousconditions tested was determined microscopically by direct cell count.Down-regulation of Survivin expression under these experimentalconditions was assessed by immunoblotting with JC700 antibody.

Example 9 Identification of EPR-1 Complementary Gene

Three overlapping clones were isolated by hybridization screening of ahuman P1 plasmid genomic library with the EPR-1 cDNA and confirmed bySouthern blot. This gene was located to the long arm of chromosome 17,to band 17q25, by fluorescence in situ hybridization (FIG. 1A, B).

A contig of P1 fragments spanning 14796 bp was cloned in pBSKS⁻ andcompletely sequenced on both strands (FIG. 1C). Three putative splicesites, matching perfectly the consensus sequences for eukaryoticintron-exon boundaries (Padgett, R. A. et al., Ann Rev Biochem (1986)55:1119-1150), were identified at position 2922, 3284, and 5276 (donor),and 3173, 5157, and 11954 (acceptor), thus defining a gene organizationin four exons and three introns of 252, 1874, and 6678 bp, respectively(FIG. 1D).

Sequence analysis of the putative coding regions demonstrated a nearlycomplete identity with the EPR-1 cDNA (Altieri, D. C., FASEB J (1995)9:860-865), except for 5 nucleotide changes and 6 nucleotide insertions.However, the three splice sites were found on the complementary,antisense strand of the EPR-1 coding sequence. Consistent with thisunexpected orientation, the EPR-1 complementary gene revealed a 5′ GCrich region, comprising nucleotides 2560-2920 and including exon 1 (seebelow), which fulfilled the base composition criteria of a CpG island(Gardiner-Garde, M. et al., J Mol Biol (1987) 196:261-282 and Frommer,1987). Sequencing the 2.5 kb upstream the CpG island revealed aTATA-less promoter with numerous SpI sites (not shown).

Complex hybridization pattern and evolutionary conservation of EPR-1sequences. Probing human genomic DNA with the EPR-1 cDNA revealedseveral hybridizing fragments (FIG. 2A). Of these, a ˜7.5 kb XbaI, a 7.6kb BamHI, and 4 HindIII fragments of ˜15, 7.5, 6.4, and 3.7 kb,respectively (FIG. 2A, arrows), could not be recapitulated by therestriction map of the antisense EPR-1 gene (FIG. 1C). In contrast,other bands of comparable intensity, including a 5.15 kb XbaI and a 7.1kb BamHI fragment, genuinely originated from the antisense EPR-1 geneand comprised the first two, or three exons, respectively (FIG. 2A).

At variance with this complex hybridization pattern, Southern blot ofhigh molecular weight human genomic DNA digested with MluI or NotI andseparated by pulsed field gel electrophoresis, revealed singleEPR-1-hybridizing bands of ˜75 kb and 130 kb, respectively (FIG. 2B).Finally, Southern blots of multiple species genomic DNA revealedsignificant evolutionary conservation of EPR-1-related sequences (FIG.2C), with numerous strongly hybridizing bands in mammalian species andfainter signals in rabbit or chicken genomic DNA, under high stringencyhybridization conditions (FIG. 2C).

Discordant tissue distribution of sense/antisense EPR-1 transcripts. Thepotential expression of distinct sense or antisense EPR-1 transcriptswas investigated in Northern blots with single strand-specific probes.Consistent with the size of the spliced EPR-1 message (Altieri, D. C.,FASEB J (1995) 9:860-865), an EPR-1 strand-specific probe detected aprominent ˜1.2 kb band in mRNA extracted from all adult andterminally-differentiated human tissues examined (FIG. 3A). In contrast,no specific bands hybridized with a EPR-1 antisense-specific singlestrand probe in adult tissues, under the same experimental conditions(FIG. 3B). A similar ˜1.2 kb band was detected by the single strandEPR-1-specific probe in fetal kidney, and, to a lesser extent, in fetalliver, lung and brain (FIG. 3A). At variance with the absence ofhybridization in adult tissues, the EPR-1 antisense-specific proberecognized a prominent ˜1.9 kb band, and a larger 3.2 kb speciescorresponding to the size of an incompletely processed transcript, infetal liver, while fainter hybridization bands were also seen in fetalkidney, lung and brain (FIG. 3B). A control hybridization with an actinprobe confirmed comparable loading of mRNA in adult or fetal samples(FIG. 3C).

Characterization of the antisense EPR-1 ene product. Inspection of the5′CpG island in the antisense EPR-1 gene revealed a putative ATGinitiation codon at position 2811, surrounded by a sequence (CGGCATGG)that conformed well to the consensus for eukaryotic initiation oftranslation (Kozak, M., Nucleic Acids Res (1984) 12:857-872). Analysisof the antisense EPR-1 sequence in the 5′→3′ direction dictated by theposition of intron-exon boundaries revealed an open reading frame of 426bp, spanning all four exons, and terminating with a TGA codon atposition 12042 in exon 4. A canonical polyadenylation signal (AATAAA)was found at position 13166. PCR products amplified fromreverse-transcribed HeLa cell RNA primed with EPR-1 “sense”oligonucleotides matched perfectly the genomic sequence and confirmedthe open reading frame and the predicted intron-exon boundaries (notshown).

Two λgt11 cDNA clones isolated by hybridization of a HEL library withthe EPR-1 cDNA, also matched the consensus genomic sequence and revealeda homopolymeric A tail on the antisense EPR-1 strand at position 13186,14 bp downstream the polyadenylation signal, generating a 3′untranslated region of 1144 bp. In these clones, the 5′ untranslatedregion upstream from the initiating ATG was of 49 bp, beginning atposition 2762 in the genomic sequence, and contained an in-frametermination codon. Translation of the antisense EPR-1 open reading framepredicted a new protein of 142 amino acids, with an estimated molecularweight of 16,389 and an acidic pI of 5.74, lacking an amino-terminussignal peptide or a carboxy terminus hydrophobic stretch for membraneinsertion (FIG. 4A).

A coiled coil was predicted for the last 40 carboxy terminus residues(Lupas, A. et al., Science (1991) 252:1162-1164). BLAST databasesearches revealed a significant degree of similarity between residues18-88 of the antisense EPR-1 gene product and the BIR module in the IAPfamily of inhibitors of apoptosis (Birnbaum, M. J. et al., J Virology(1994) 68:2521-2528; Clem, R. J. et al., Mol Cell Biol (1994)14:5212-5222). For this analogy, the antisense EPR-1 gene product wasdesignated Survivin. At variance with other IAP proteins, Survivincontained only one BIR, encoded by the first three exons of the gene,and lacked a carboxy terminus RING finger, withoutadditional/alternative exon(s) potentially encoding this domain (FIG.1C).

An alignment by the Clustal method between the Survivin BIR and that ofother known IAP proteins is shown in FIG. 4B. Despite the overall matchof the consensus and several conservative substitutions, phylogeneticanalysis suggested that Survivin is a distantly related member of theIAP family, most closely related to NAIP, which also lacked a RINGfinger (FIG. 4B, shaded boxes) (Roy, N. et al., Cell (1995) 80:167-178).

A rabbit polyclonal antiserum designated JC700, was raised againstresidues A ³PTLPPAWQPFLKDHRI¹⁹ (SEQ ID NO: 3) of Survivin, purified byaffinity chromatography on a peptide-Sepharose column, and used inWestern blots. Consistent with the predicted molecular weight ofSurvivin, JC700 antibody immunoblotted a single band of ˜16.5 kDa fromdetergent-solubilized extracts of all transformed cell lines examined,including B lymphoma Daudi and JY, T leukemia Jurkat and MOLT13,monocytic THP-1, and erythroleukemia HEL (FIG. 4C).

Survivin was also found in isolated peripheral blood mononuclear cells(PBMC). In contrast, no expression of Survivin was detected innon-transformed Lu-18 human lung fibroblasts or human umbilical veinendothelial cells (HUVEC) (FIG. 4C). No specific bands wereimmunoblotted by control non-immune rabbit IgG, under the sameexperimental conditions (FIG. 4C).

Identification of agents that modulate transcription of the EPR-1 gene.Agents that increase the transcription of the EPR-1 gene may beidentified by conventional techniques. Preferably, a candidate agent isbrought into contact with a cell that expresses the EPR-1 gene productand the level of expression of this product or the level oftranscription are determined and agents that increase or decrease EPR-1gene transcripts may readily be identified. Alternatively, the EPR-1transcriptional regulatory elements may be placed upstream of a reportergene such as CAT or β-galactosidase.

Example 10 Regulation of Survivin Expression by CellGrowth/Differentiation

Consistent with the expression of Survivin in transformed cell lines(FIG. 4C), undifferentiated and actively proliferating promyelocyticHL-60 cells constitutively expressed high levels of Survivin, asdemonstrated by immunoblotting of a single ˜16.5 kDa band with JC700antibody, and Northern hybridization of a ˜1.9 kb transcript with asingle strand-specific probe (FIG. 5). In contrast, no specific bandswere recognized by control non-immune rabbit IgG under the sameexperimental conditions (FIG. 5).

Vitamin D₃-induced terminal differentiation of HL-60 cells to a maturemonocytic phenotype resulted in growth arrest of these cells and de novoinduction of differentiation-specific markers, including a ˜200-foldincreased expression of leukocyte CD11b/CD18 integrin detected by flowcytometry (not shown), and in agreement with previous observations(Hickstein, D. D. et al., J Immunol (1987) 138:513-519). Under theseexperimental conditions, the anti-Survivin JC700 antibody failed toimmunoblot specific bands from vitamin D₃-treated HL-60 extracts, and noSurvivin transcript(s) were detected by Northern hybridization with asingle strand-specific probe (FIG. 5).

In contrast, an anti-EPR-1 polyclonal antibody immunoblotted a single˜62 kDa band corresponding to EPR-1 in vitamin D₃-differentiated HL-60extracts under the same experimental conditions (not shown). Moreover,down-regulation of Survivin in vitamin D₃-differentiated HL-60 cells wasaccompanied by a 5- to 10-fold increased surface expression of EPR-1 inthese cells, as detected by flow cytometry with anti-EPR-1 monoclonalantibodies B6 or 12H1 (FIG. 8).

As shown in FIG. 16, Survivin is down regulated by the combination ofcytokines y interferon and tumor necrosis factor α, but not by eithercytokine alone. Similarly, the transfection of 3T3 cells with the c-myconcogene results in the up-regulation of Survivin mRNA as detected byNorthern blots.

Example 11 Promoting Apoptosis with Survivin

Targeting Survivin promotes apoptosis and inhibits cell proliferation.Transfection of the Survivin cDNA in mouse or hamster cell lines (NIH3T3, CHO) was not suitable for the presence of immunochemicallyindistinguishable endogenous homologues in these cells (not shown).Similarly, initial attempts to target the Survivin gene in stableantisense transfectants were unsuccessful for slow cell growth and rapidloss of viability (not shown). Therefore, Survivin⁺ HeLa cells weretransfected with the 3′ end of the EPR-1 cDNA (Survivin antisense) underthe control of a metallothionein-inducible promoter (Lukashev, M. E. etal., J Biol Chem (1994) 269:18311-18314), selected in hygromycin, andanalyzed for apoptosis and cell proliferation after Zn²⁺-dependentactivation of transcription.

Consistent with the expression of Survivin in transformed cell lines(FIG. 4C), the JC700 antibody immunoblotted a single molecular speciesof ˜16.5 kDa in extracts of control HeLa cells transfected with thevector alone (FIG. 7A). In contrast, no specific bands were recognizedby JC700 antibody in metallothionein-induced HeLa cells transfected withthe EPR-1 cDNA (Survivin antisense) (FIG. 7A). Under these experimentalconditions, in situ analysis of internucleosomal DNA fragmentation byAptoTag staining revealed only a few apoptotic cells in serum-starved,Zn²⁺-induced, vector control HeLa cells (FIG. 7B).

In contrast, as discussed above, inhibition of Survivin expression inZn²⁺-induced antisense HeLa cell transfectants was associated withprominent nuclear staining in the vast majority of cells examined (FIG.7B). No nuclear staining was detected in the absence of TdT tagging ofthe digoxigenin-labeled dUTP (not shown). Typical morphologic featuresof apoptosis, including numerous apoptotic bodies, were alsodemonstrated in induced antisense HeLa cell transfectants byhematoxylin/eosin staining, while only occasional apoptotic bodies wereobserved in vector control HeLa cultures, under the same experimentalconditions (FIG. 7B).

A potential effect of Survivin on cell growth was also investigated. Inthese experiments, metallothionein-controlled, EPR-1-dependent,inhibition of Survivin expression caused a profound reduction ofserum-dependent HeLA cell proliferation (FIG. 7C). Three days after Zn²⁺induction, the cell count in vector control HeLa cultures increased by288%, as opposed to only a 20% increase in Survivin antisensetransfectants, under the same experimental conditions (FIG. 7C).

Example 12 Structure—Function Relationship of Survivin

The minimal structural requirements involved in Survivin-mediatedinhibition of apoptosis have been identified through a mutagenesisstrategy of Ala substitutions of the most evolutionarily conservedresidues in the single Survivin BIR (baculovirus IAP repeat) module.These residues included in the amino-terminal half of the Survivin BIR,Arg¹⁸, Phe²², Trp²⁵, Pro²⁶, Pro³⁵, Ala³⁹, Ala⁴¹, Gly⁴², and Cys⁴⁶. Inthe carboxyl-terminal half of the Survivin BIR, Ala mutants were firsttargeted at the Cys⁵⁷X₂Cys⁶⁰X₁₆His⁷⁷X₆Cys⁸⁴ putative zinc binding motif.Additional conserved residues targeted by mutagenesis include Asp⁵³,Leu⁶⁴, Trp⁶⁷, Pro⁶⁹, Asp⁷¹, Asp⁷² and Pro⁷³.

The Survivin mutants are characterized in stable and transientlytransfected cells, IL-3-dependent BaF3 cells and NIH3T3, respectively.In addition to these point mutants, a Survivin chimeric moleculecontaining a carboxyl-terminal RING finger has also been generated andscreened for apoptosis inhibition (the RING finger is a domain found inmost other IAP proteins, but not in Survivin). Secondly, a truncatedform of Survivin has also been generated, in which the last 40carboxylterminus residues, containing a predicted coiled-coil structure,have been deleted. As shown in FIG. 12, Ala mutagenesis of key conservedresidues in Survivin Trp⁶⁷-Pro⁷³-Cys⁸⁴ produced a recombinant moleculewhich lacked the ability to protect BaF3 cells from apoptosis induced byIL-3 withdrawal.

Example 13 Cytoprotective Effects of Survivin

Classical examples of cell damage to stable cell populations mediated byapoptosis include allograft rejection by infiltrating lymphocytes,Alzheimer's disease and reperfusion injury following myocardialinfarction. In addition to being expressed in cancer, therebyfunctioning as a growth-advantage factor for cancer cells, the targetedexpression of Survivin is useful to protect stable cell populations fromapoptosis and other cellular insults. This application of Survivin wastested by adding increasing concentrations of purified recombinantSurvivin to monolayers of human endothelial cells injured with hydrogenperoxide (H₂O₂), a classical apoptosis-inducing stimulus. The resultsare summarized in FIG. 13. Increasing concentrations of added Survivinresulted in a significant increased viability of the treated cells asopposed to control cultures treated with control protein myoglobin.Similarly, Survivin protected NIH3T3 cells from apoptosis induced byhydrogen peroxide after transient co-transfection with a lacZ reportergene as shown in FIG. 17.

Example 14 Survivin as a Predictive-Prognostic Factor

The presence of Survivin can be utilized as predictive-prognosticnegative factor in neuroblastoma and non-Hodgkin's lymphoma, and inother cancers.

Neuroblastoma. A large series of neuroblastoma cases (72) was screenedfor Survivin expression in a multicentric study. As shown in FIG. 14,Survivin expression increased dramatically when patients contained atleast one negative prognostic factor for aggressive and rapidlyprogressing disease. Secondly, expression of Survivin stronglycorrelated with a more aggressive disease and unfavorable histology.Importantly, expression of Survivin was a more sensitive prognosticindex than simple histology. Survivin-positive cases with earlydiagnosis of favorable histology were found to contain at least onenegative prognostic factor for disease progression and dissemination.

Hodgkin's Lymphoma. A similar multicentric study has been recentlycompleted on analysis of Survivin expression in high grade non-Hodgkin'slymphoma (n=48). The results are similar to those observed forneuroblastoma. As shown in FIG. 15, expression of Survivin stronglycorrelated with a more widespread disease predominantly in stage IV.Clinically, Survivin-expressing patients had fewer episodes of completeremission and more episodes of incomplete remission, no remission orrelapses as compared with Survivin-negative patients.

Potential implications. The demonstrated role of Survivin as a negativepredictive prognostic factor in these two embryologically differenttypes of cancer iterates the potential use of this molecules adiagnostic tool to monitor disease progression and response to thetherapy. It can also be used for staging purposes and to identifypopulations of patients potentially susceptible to multi-drug resistance(groups with no remissions or incomplete remissions). Also, Survivinderived primers easily designed from the complete sequence of theSurvivin gene can be used as a screening tool to identify potentialcases of cancer in which the Survivin gene has been deleted or mutated.These cases will be very important to identify because targetedinactivation of the Survivin gene would confer a favorable prognosticfactor to cancer patients, removing a potential drug-resistance gene.Inactivating mutations in the Survivin gene can target the same keyresidues identified in our initial screening of Ala-based mutagenesis orresult in an abortive or truncated protein for premature termination oftranslation.

Example 15 Survivin Cancer Vaccine

Vaccines directed against Survivin, as found in various types of cancer,may be developed as with other disease-related intracellular proteintargets. These techniques are commonly available and representativeapproaches are described by the references cited below. Vaccines mayalso include the systemic administration of peptide fragments ofSurvivin and the use of vectors to deliver mini-genes encoding Survivinpeptides to tumor cell targets are contemplated. As mentioned above,Survivin is not expressed in normal cells, even in proliferating stemcells in the bone marrow. This ensures that the immune response mountedagainst Survivin will be highly selective and specific and will notinvolve normal cells.

Development and Administration of Polypeptide-Based Vaccines

Methods of the use of peptide components in a monovalent or a polyvalentcancer immunotherapy-vaccine product are described by Nardi, N. et al.,Mol. Med. (1995) 1(5):563-567. Additional references that discuss thedifferent cancer vaccine and cancer immunotherapies currently being usedinclude: N. P. Restifo and M. Sznol “Cancer Vaccines,” in DeVita'sCancer: Principles & Practice of Oncology 3023-3043 (Lippincott-Raven,Philadelphia; 1997); J. Galea-Lauri et al., Cancer Gene Ther. (1996)3(3): 202-214; D. C. Linehan et al., Ann. Surg. Oncol. (1996) 3(2):219-228; and J. Vieweg et al., Cancer Invest. (1995) 13(2): 193-201.

Consistent with the foregoing approach, Survivin polypeptides or fulllength Survivin are synthesized either chemically by known techniques orrecombinantly by expressing appropriate cDNAs in prokaryotic oreukaryotic cells. Survivin proteins so produced are then purified asnecessary to remove contaminating proteins, such as serum or bacterialproteins. Survivin can be further purified using columns containingantibodies that bind Survivin, such as the monoclonal antibody JC700 orthe antibody 8E2 (both described above) which recognize and bind toSurvivin. In purifying an antibody-based vaccine, the recombinantlyproduced Survivin would bind to the antibodies while other proteins andcellular debris would be washed out. Survivin polypeptides are then beisolated and concentrated to a desired strength.

Alternatively Survivin polypeptides are created by cleaving the nativeSurvivin with one or more proteases (e.g., trypsin). Proteolyticfragments are then separated and recovered using SDS-PAGE,high-resolution/high-pressure separation techniques, or reverse-phaseHPLC. See R. J. BEYNON AND J. S. BOND, PROTEOLYTIC ENZYMES: A PRACTICALAPPROACH (Oxford University Press, New York 1989). These isolatedpeptides are then concentrated to a desired final concentration.

Once purified, Survivin polypeptides or full length Survivin moleculesmay then be placed in an emulsion containing an adjuvant. Adjuvantscontemplated for use with Survivin include aluminum adjuvants, Freund'sadjuvant, oil-in-water emulsions containing tubercle bacilli, andinterleukin-2 (IL-2). Additional preparations include combining theSurvivin polypeptides with other appropriate tumor-associated antigensand, optionally, other immunomodulatory agents such as cytokines. Othersuitable carriers or excipients can be used including bovine serumalbumin, coupling the Survivin polypeptide with haptens, keyhole limpethemocyanin, ovalbumin, and purified protein derivative of tuberculin.Peptides may be coupled to carriers using techniques such as thosedescribed in ED HARLOW AND DAVID LANE, ANTIBODIES: A LABORATORY MANUAL(Cold Spring Harbor Laboratory, 1988).

Vaccines in human subjects may be administered in the form of anemulsion injected subcutaneously, intradermally or intramuscularly (IM);vaccines appropriately formulated can be taken orally. With vaccinescontaining adjuvants, the vaccine is generally preferably be given IM,e.g., in the deltoid.

The amount of Survivin vaccine or Survivin peptide vaccine to beadministered to a patient will correspond to values typically used infor other cancer vaccines. Dosage concentrations will range from about0.25 g to about 1000 g per day. More preferred ranges will be from about10 μg to about 500 μg per day.

Example 16 Diagnostic Use of Anti-Survivin Antibodies

Frequently, tumor associated antigens (TAA) are shed from tumor cellsinto the surrounding plasma or into the blood. As a result, TAA oftenare found in the blood, and blood samples obtained from patients may beused in detecting the presence of cancer, as well as used as a factor isstaging cancers (e.g., stage I, II, III or IV). Survivin is one suchTAA, and healthy, normal individuals do not express Survivin. Resultsfrom studies of several cancers have indicated that the presence ofSurvivin (or Survivin fragments) correlates with and is predictive thatthe disease may be aggressive or may have metastasized. A similarstrategy of detecting and quantifying the levels of Survivin or Survivinfragments can be used to determine residual tumor burden in patientsundergoing chemotherapy or radiation therapy for cancer treatment.Elevated or increasing levels of Survivin may reflect late stageneoplastic disease.

For diagnostic uses, blood is drawn from patients, by well knowntechniques, who have known cancer loads or from patients suspected ofhaving cancer. The blood sample is prepared by known techniques and istested for binding with antibodies to Survivin that are prepared and,optionally, labeled, as discussed above. Such general antibody detectionprotocols and associated reagents are well established in the art. Otherbiological fluid samples such as semen, urine, or saliva can also bemonitored for the presence of Survivin. This diagnostic technique alsocan be used to monitor disease progression and response toindividualized therapies. This method offers a relatively non-invasivemeans of tracking cancer progression or regression.

Example 17 Detection of Survivin by Immunobioassay

An illustrative example of an immunobioassay to test for the presence ofSurvivin in the blood of patient relies on the ability of the monoclonalantibodies to Survivin to bind Survivin and remove the detectableSurvivin from solution by immunoprecipitation. Such an immunobioassay isused to detect Survivin in suspected cancer patients and in fractionseluted from fractionation columns. An aliquot of each patient sample isincubated for 2 hours at 4° C. with a monoclonal antibody thatspecifically recognizes and binds Survivin, such as the Mab 8E2,described above. The monoclonal antibody is insolubilized on anti-mouseIgG agarose beads, which can be acquired from Sigma Chemical Co., St.Louis, Mo.

The agarose bead anti-mouse (IgG(H+ L))-Survivin complex is prepared byfirst washing the agarose beads with binding buffer containing 0.01 Mphosphate buffer, (pH 7.2), and 0.25 M NaCl and then incubating thebeads with the Survivin monoclonal antibody for 18 hours at 4° C. in thesame buffer. The agarose beads may then be sedimented by centrifugationfor 30 seconds at 16,000×g in a microcentrifuge and non-specific sitesmay be blocked by incubation with 2% non-fat dry milk in 0.5 M NaCl-TMKfor 30 minutes at 4° C. After blocking, the beads may be washed 3 timeswith 0.5 M NaCl-TMK and resuspended in an equal volume of the samebuffer. 20:1 of the agarose bead-monoclonal antibody complex may thenincubated with each 250:1 of the patient test sample for 2 hours at 4°C. Any Survivin present in the patient test sample will be found by theSurvivin monoclonal antibody on the beads. The bead complex, now withSurvivin bound, may be removed by centrifugation for 30 seconds at16,000×g. The supernatant is then assayed for Survivin activity in thebioassay as described below. Control samples are treated with blockedbeads that lacked the Survivin monoclonal antibody and tested forSurvivin activity in the bioassay.

Example 18 Detecting Survivin Using a Direct Elisa Test

Samples of normal plasma (control) and cancer patient-plasma are diluted1:1 with phosphate buffered saline (PBS). One volume of each mixture isadded to centricon-10 filter having a 10 kD molecular weight limit andcentrifuged at 5000×g (7000 rpm) for 1 hour. One volume of PBS is addedto the retentate and centrifuged for 30 min. The final dilution is about1:3. The ELISA plate wells are then coated with retentate at 1:6, 1:12,1:24, 1:48 and 1:96 final dilution in bicarbonate coating buffer, havinga pH 9.6 overnight at 4° C. C. The plates are then washed 2 times withwash buffer containing 5% Tween 20 in phosphate buffered saline.Residual binding sites are blocked with 4% bovine serum albumin (BSA),300μ/well for 2 hours. Plates are then washed 2 times with wash buffer.Next, 100 μl of a monoclonal antibody that specifically recognizes andbinds to Survivin, such as Mab 8E2, is used at 1:200 dilution in 1% BSAis added to the wells and incubated for 1 hour with agitation. Platesare washed 5 times with wash buffer. Next, 100 μl horseradish peroxidaseconjugated secondary antibody is added, typically at a 1:2,000 dilutionto each well, and incubated for 1 hour. Plates are again washed 5 timeswith wash buffer. Next, 100 μl/well of substrate containing 5 μg ofSurvivin and 5 μl H₂O₂/10 ml citrate-phosphate buffer is added to eachwell and incubated for 5 minutes. The enzyme reaction is stopped byadding 50 μl/well 2 M H₂SO₄. The absorbance of light is measured at 492nm in an EIA reader. Patient samples that contain Survivin will producea positive reading, whereas those samples that do not contain Survivinwill be negative.

Example 19 Survivin Fragments, Peptides and Small Molecule Antagonists

As described above, key functional residues in Survivin required forapoptosis have been identified. These data provide a template upon whichto produce synthetic peptides and small molecule antagonists andcompetitive inhibitors of Survivin function. Preferably, the peptidesare produced from native Survivin or include substitutions from thenative Survivin peptide backbone that include the functionally relevantresidues Trp⁶⁷-Pro⁷³-Cys⁸⁴. Peptide fragments of native Survivin can begenerated by standard techniques, including protein digests. Adetermination of which fragments compete with Survivin can readily bemade by using the apoptosis measurement systems and apoptosis assaysystems described above. These results provide a unique opportunity toidentify a discrete linear sequence in Survivin that is essential forinhibition of apoptosis.

Consistent with the general paradigm of IAP proteins-dependentinhibition of apoptosis, it also was predicted that a structural regionin the molecule required for the anti-apoptotic function is the primarycandidate for being a site of interaction with other molecules (such asbinding partners). The functionally relevant peptide sequence inSurvivin, based on the mutagenesis data, is: EGWEPDDDPIEEHKKHSSGC (SEQID NO: 4). Ala substitutions of the underlined residues results in acomplete loss of function of Survivin in transfected cells. This linearsequence can be synthesized and used as a much more stringent andspecific reagent to isolate associated molecules using standardbiochemical procedures of affinity chromatography or as a bait for theyeast two-hybrid system.

Also, preferably, the βCOOH coiled-coil region of Survivin is includedin Survivin fragments and peptides. Recent data indicates that thisSurvivin domain is important for the anti-apoptosis function ofSurvivin. We have generated a recombinant truncated form of Survivinlacking the last 40 βCOOH terminus amino acids comprising thecoiled-coil domain. This truncated form was co-transfected with a lacZplasmid in NIH3T3 cells side-by-side with wild type Survivin and XIAP,another member of the LAP gene family. The results, shown in FIG. 17,indicate that the truncated Survivin had lost most (˜80%) of thecytoprotective effect at preventing apoptosis in transfected cellsinduced by hydrogen peroxide. Incidentally, in this system, Survivin wasmore potent than NAIP at preventing apoptosis.

Agonists and antagonists of Survivin also can readily be identifiedthrough conventional techniques. Designed, synthetic peptides based onthe native linear sequence also function as competitive inhibitors ofSurvivin's interaction with as yet unidentified partner molecules.However, this inhibition should be sufficient to block theanti-apoptosis function of Survivin.

A similar peptide-based strategy has been successful to block caspaseactivation in vitro and in vivo, protecting cells from apoptosis. See,e.g., Milligan, C. E. et al., (1995) Neuron 15:385-393.

Example 20 Therapeutic Uses of Antisense Survivin DNA

As described above, the transcription of a Survivin antisense sequencealtered the EPR-1/Survivin gene balance. This was demonstrated in HeLacell transfectants, in which metallothionein-induced transcription ofthe EPR-1 “sense” strand suppressed the expression of Survivin andprofoundly influenced apoptosis/cell proliferation. Additionally,transiently co-transfecting a Survivin antisense construct with a lacZreported plasmid decreased the viability of Survivin antisensetransfectants after a 48-h transfection in β-galactosidase expressingcells. Accordingly, the level of expression of Survivin in a Survivinexpressing cell or tissue, such as a tumor, is decreased by transfectingthe cell or tissue with the EPR-1 sense strand of DNA. Alternatively, aSurvivin antisense-encoding DNA is used to transfect a target cell ortissue. Such therapy effectively decreases the translation ofSurvivin-encoding mRNA into Survivin protein.

Example 21 Use of Survivin as a Protective Agent Against Apoptosis

Survivin has been shown to protect cells from apoptosis whenadministered to cells that have been exposed to hydrogen peroxide orother agents that typically induce apoptosis. It is contemplated thatcellular permeability may need to be increased, preferably in atransient manner in order to facilitate delivery of Survivin, orfragments thereof effective to reduce apoptosis. Certain conditionsinvolving transient metabolic inhibition or transient hypoxia are likelyto increase cellular permeability without the need for additional,external agents. Agents that may be appropriate include, metabolicinhibitors like 2-deoxygluocose and sodium azide. However, the abilityof Survivin to mediate cytoprotection during a transient increase incellular permeability offers the possibility of using therapeuticinfusion of recombinant Survivin to decrease reperfusion injury andcellular damage during myocardial infarction and stroke. It iscontemplated that such processes are mediated by increased tissue damagedue to apoptosis. Treatment with Survivin could reduce the extent andmagnitude of the injured tissue.

The use of Survivin or allelic variants of Survivin in subjects tomodulate or prevent apoptosis related cell death would be beneficial intreating or ameliorating the effects of a variety of apoptosis-relatedindications. These indications include, but are not limited to,dermatological effects of aging (e.g., baldness that is caused byapoptosis of cells of hair follicle cells), disorders and diseases suchas immunosuppression, gastrointestinal perturbations (e.g., damage oflining of the gut, ulcers, and radiation or chemotherapy induceddamage), cardiovascular disorders, apoptosis related to reperfusiondamage (e.g., coronary artery obstruction, cerebral infarction,spinal/head trauma and concomitant severe paralysis, damage due toinsults such as frostbite or burns, and any indication previouslythought to be treatable by superoxide dismutase), rejection of tissuetransplantation (e.g., graft versus host disease), and Alzheimer'sdisease. The administration of Survivin also may be cytoprotectiveagainst chemotherapy or radiation-induced apoptosis.

Survivin protein for administration can be produced as described above,e.g., using the cDNA described herein. The protein may requirepurification for purposes of pharmaceutical administration and suchpurification steps preferably utilize monoclonal antibody separation andpurification techniques as also described above.

In a clinical setting, Survivin is administered to patients inpharmaceutically effective dosages, i.e., in dosages effective to reducethe level or extent of apoptosis otherwise present, via several routes.For example, to treat dermatological ailments that involve apoptosis,Survivin can be administered in a salve, cream, ointment or powder form.Topical formulations may contain additional pharmaceutical or cosmeticcompositions such as moisturizers, humectants, odor modifiers, buffer,pigment, preservatives, vitamins (such as A, C or E), emulsifiers,dispersing agents, wetting agents, stabilizers, propellants,antimicrobial agents, sunscreen, enzymes and the like. Typical dosagesof Survivin that may be administered to patients will be 0.01% to 1.0%by weight. Additional topical pharmaceutical compositions are describedin S. Nakai et al., U.S. Pat. No. 5,672,603.

Survivin may also be administered, as may be appropriate for thecondition being treated, in the form of pills, solutions, suspensions,emulsions, granules or capsules. Survivin can be administered orally;injected in solutions administered intravenously either alone or inadmixture with conventional fluids for parenteral infusion (e.g., fluidscontaining glucose, amino acids etc.); injected intramuscularly,intradermally, subcutaneously or intraperitoneally; using suppositories;and in the form of ophthalmic solutions such as eye drops. Survivin canalso be administered using delayed release carriers, such as liposomes,microsponges, microspheres or microcapsules that are deposited in closeproximity to the tissue being treated for prevention of apoptosisrelated cell death.

Concentrations of Survivin or functional allelic variants of Survivinadministered via routes other than topical administration typicallywould range in dose from about 10 μg per day to about 25 mg per daydepending on the route of administration. Of course, it would beexpected that skilled artisans, such as physicians, may alter thesevalues on a case by case basis as required for the particular patient.

1-59. (canceled)
 60. An oligonucleotide that hybridizes under stringentconditions with a polynucleotide having the sequence SEQ ID NO: 35, butdoes not hybridize under stringent conditions with a polynucleotidehaving the sequence of human EPR-1 mRNA, wherein the stringentconditions are selected from the group consisting of: (1) washing with0.015 M sodium chloride, 0.0015 M sodium titrate, 0.1% SDS at 50° C.;(2) hybridization in 50% (vol/vol) formamide with 0.1% bovine serumalbumin, 0.1% Ficoll, 0.1% polyvinylpyrrolidone, 50 mM sodium phosphatebuffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at42° C.; and (3) hybridization in 50% formamide, 5×SSC (0.75 M sodiumchloride, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1%sodium pyrophosphate, 5× Denhardt's solution, sonicated salmon sperm DNA(50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at42° C. in 0.2×SSC and 0.1% SDS, or the complement of saidoligonucleotide.
 61. The oligonucleotide of claim 60 or its complement,wherein the oligonucleotide is a DNA oligonucleotide.
 62. Theoligonucleotide of claim 60 or its complement, wherein theoligonucleotide is extendable by a polymerase enzyme.
 63. Theoligonucleotide of claim 60 or its complement, comprising a detectablelabel.
 64. A kit for amplifying an mRNA encoding survivin, the kitcomprising a first extendable primer that hybridizes under stringentconditions with the mRNA and at least one second primer that hybridizesunder stringent conditions with an antisense strand of the mRNA, whereinat least one of the first and second primers is an oligonucleotide ofclaim 60 or its complement.
 65. A kit for amplifying an mRNA encodingsurvivin, the kit comprising a first extendable primer that hybridizesunder stringent conditions with the mRNA and at least one second primerthat hybridizes under stringent conditions with an antisense strand ofthe mRNA, wherein each of the first and second primers is anoligonucleotide of claim 60 or a complement thereof.
 66. A method ofdetecting expression of survivin in a sample obtained from a human, themethod comprising using the oligonucleotide of claim 60, or itscomplement, as a primer in a reverse-transcriptase amplification methodfor amplifying mRNA encoding survivin.
 67. An oligonucleotide thathybridizes under stringent conditions with a polynucleotide having thesequence of the coding sequence of survivin, but does not hybridizeunder stringent conditions with a polynucleotide having the sequence ofthe coding sequence of human EPR-1, wherein the stringent conditions areselected from the group consisting of: (1) washing with 0.015 M sodiumchloride, 0.0015 M sodium titrate, 0.1% SDS at 50° C.; (2) hybridizationin 50% (vol/vol) formamide with 0.1% bovine serum albumin, 0.1% Ficoll,0.1% polyvinylpyrrolidone, 50 mM sodium phosphate buffer at pH 6.5 with750 mM sodium chloride, 75 mM sodium citrate at 42° C.; and (3)hybridization in 50% formamide, 5×SSC (0.75 M sodium chloride, 0.075 Msodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodiumpyrophosphate, 5× Denhardt's solution, sonicated salmon sperm DNA (50μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42°C. in 0.2×SSC and 0.1% SDS, or the complement of said oligonucleotide.68. The oligonucleotide of claim 67 or its complement, wherein theoligonucleotide is a DNA oligonucleotide.
 69. The oligonucleotide ofclaim 67 or its complement, wherein the oligonucleotide is extendable bya polymerase enzyme.
 70. The oligonucleotide of claim 67 or itscomplement, comprising a detectable label.
 71. The oligonucleotide ofclaim 67 or its complement, wherein the coding sequence of survivin hasthe sequence of nucleotides 2811-2921 directly attached to nucleotides3174-3283 directly attached to nucleotides 5158-5275 directly attachedto nucleotides 11955-12044 of SEQ ID NO:
 35. 72. A kit for amplifying anmRNA encoding survivin, the kit comprising a first extendable primerthat hybridizes under stringent conditions with the mRNA and at leastone second primer that hybridizes under stringent conditions with anantisense strand of the mRNA, wherein at least one of the first andsecond primers is an oligonucleotide of claim 67 or its complement. 73.A kit for amplifying an mRNA encoding survivin, the kit comprising afirst extendable primer that hybridizes under stringent conditions withthe mRNA and at least one second primer that hybridizes under stringentconditions with an antisense strand of the mRNA, wherein each of thefirst and second primers is an oligonucleotide of claim 67 or acomplement thereof.
 74. A method of detecting expression of survivin ina sample obtained from a human, the method comprising using theoligonucleotide of claim 67, or its complement, as a primer in areverse-transcriptase amplification method for amplifying mRNA encodingsurvivin.
 75. An oligonucleotide that hybridizes under stringentconditions with the mRNA encoding human survivin, but does not hybridizeunder stringent conditions with the mRNA encoding human EPR-1, whereinthe stringent conditions are selected from the group consisting of: (1)washing with 0.015 M sodium chloride, 0.0015 M sodium titrate, 0.1% SDSat 50° C.; (2) hybridization in 50% (vol/vol) formamide with 0.1% bovineserum albumin, 0.1% Ficoll, 0.1% polyvinylpyrrolidone, 50 mM sodiumphosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodiumcitrate at 42° C.; and (3) hybridization in 50% formamide, 5×SSC (0.75 Msodium chloride, 0.075 M sodium citrate), 50 mM sodium phosphate (pH6.8), 0.1% sodium pyrophosphate, 5× Denhardt's solution, sonicatedsalmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42°C., with washes at 42° C. in 0.2×SSC and 0.1% SDS, or the complement ofsaid oligonucleotide.
 76. The oligonucleotide of claim 75 or itscomplement, wherein the oligonucleotide is a DNA oligonucleotide. 77.The oligonucleotide of claim 75 or its complement, wherein theoligonucleotide is extendable by a polymerase enzyme.
 78. Theoligonucleotide of claim 75 or its complement, comprising a detectablelabel.
 79. A kit for amplifying an mRNA encoding survivin, the kitcomprising a first extendable primer that hybridizes under stringentconditions with the mRNA and at least one second primer that hybridizesunder stringent conditions with an antisense strand of the mRNA, whereinat least one of the first and second primers is an oligonucleotide ofclaim 75 or its complement.
 80. A kit for amplifying an mRNA encodingsurvivin, the kit comprising a first extendable primer that hybridizesunder stringent conditions with the mRNA and at least one second primerthat hybridizes under stringent conditions with an antisense strand ofthe mRNA, wherein each of the first and second primers is anoligonucleotide of claim 75 or a complement thereof.
 81. A method ofdetecting expression of survivin in a sample obtained from a human, themethod comprising using the oligonucleotide of claim 75, or itscomplement, as a primer in a reverse-transcriptase amplification methodfor amplifying mRNA encoding survivin.